Sample records for artificially degraded dna

  1. Assessing PreCR™ repair enzymes for restoration of STR profiles from artificially degraded DNA for human identification. (United States)

    Robertson, James M; Dineen, Shauna M; Scott, Kristina A; Lucyshyn, Jonathan; Saeed, Maria; Murphy, Devonie L; Schweighardt, Andrew J; Meiklejohn, Kelly A


    Forensic scientists have used several approaches to obtain short tandem repeat (STR) profiles from compromised DNA samples, including supplementing the polymerase chain reaction (PCR) with enhancers and using procedures yielding reduced-length amplicons. For degraded DNA, the peak intensities of the alleles separated by electrophoresis generally decrease as the length of the allele increases. When the intensities of the alleles decrease below an established threshold, they are described as drop-outs, thus contributing to a partial STR profile. This work assesses the use of repair enzymes to improve the STR profiles from artificially degraded DNA. The commercial PreCR™ repair kit of DNA repair enzymes was tested on both purified DNA and native DNA in body fluids exposed to oxidizing agents, hydrolytic conditions, ultraviolet (UV) and ionizing radiation, and desiccation. The strategy was to restrict the level of DNA damage to that which yields partial STR profiles in order to test for allele restoration as opposed to simple allele enhancement. Two protocols were investigated for allele restoration: a sequential protocol using the manufacturer's repair procedure and a modified protocol reportedly designed for optimal STR analysis of forensic samples. Allele restoration was obtained with both protocols, but the peak height appeared to be higher for the modified protocol (determined by Mann-Kendall Trend Test). The success of the approach using the PreCR™ repair enzymes was sporadic; it led to allele restoration as well as allele drop-out. Additionally, allele restoration with the PreCR™ enzymes was compared with restoration by alternative, but commonly implemented approaches using Restorase™, PCRBoost™, bovine serum albumin (BSA) and the Minifiler™ STR system. The alternative methods were also successful in improving the STR profile, but their success also depended on the quality of the template encountered. Our results indicate the PreCR™ repair kit may

  2. Analysis of artificially degraded DNA using STRs and SNPs--results of a collaborative European (EDNAP) exercise

    DEFF Research Database (Denmark)

    Dixon, L A; Dobbins, A E; Pulker, H K


    Recently, there has been much debate about what kinds of genetic markers should be implemented as new core loci that constitute national DNA databases. The choices lie between conventional STRs, ranging in size from 100 to 450 bp; mini-STRs, with amplicon sizes less than 200 bp; and single nucleo...

  3. Single gene retrieval from thermally degraded DNA

    Indian Academy of Sciences (India)

    Lianwen Zhang; Lianwen Zhang


    To simulate single gene retrieval from ancient DNA, several related factors have been investigated. By monitoring a 889 bp polymerase chain reaction (PCR) product and genomic DNA degradation, we find that heat and oxygen (especially heat) are both crucial factors influencing DNA degradation. The heat influence, mainly represented by temperature and heating time, affects the DNA degradation via DNA depurination followed by cleavage of nearby phosphodiesters. The heating time influence is temperature-dependent. By reactive oxygen species (ROS) scavenging and 1,3-diphenyl-isobenzofuran (DPBF) bleaching experiments the influence of oxygen on DNA thermal degradation was shown to occur via a singlet oxygen pathway. A comparative study of the thermal degradation of cellular DNA and isolated DNA showed that cellular lipids can aggravate DNA thermal degradation. These results confirm the possibility of gene amplification from thermally degraded DNA. They can be used to evaluate the feasibility of the retrieval of single gene from ancient remains.

  4. Programmable DNA-Guided Artificial Restriction Enzymes. (United States)

    Enghiad, Behnam; Zhao, Huimin


    Restriction enzymes are essential tools for recombinant DNA technology that have revolutionized modern biological research. However, they have limited sequence specificity and availability. Here we report a Pyrococcus furiosus Argonaute (PfAgo) based platform for generating artificial restriction enzymes (AREs) capable of recognizing and cleaving DNA sequences at virtually any arbitrary site and generating defined sticky ends of varying length. Short DNA guides are used to direct PfAgo to target sites for cleavage at high temperatures (>87 °C) followed by reannealing of the cleaved single stranded DNAs. We used this platform to generate over 18 AREs for DNA fingerprinting and molecular cloning of PCR-amplified or genomic DNAs. These AREs work as efficiently as their naturally occurring counterparts, and some of them even do not have any naturally occurring counterparts, demonstrating easy programmability, generality, versatility, and high efficiency for this new technology.

  5. Degradation of artificial sweeteners via direct and indirect photochemical reactions. (United States)

    Perkola, Noora; Vaalgamaa, Sanna; Jernberg, Joonas; Vähätalo, Anssi V


    We studied the direct and indirect photochemical reactivity of artificial sweeteners acesulfame, saccharin, cyclamic acid and sucralose in environm entally relevant dilute aqueous solutions. Aqueous solutions of sweeteners were irradiated with simulated solar radiation (>290 nm; 96 and 168 h) or ultraviolet radiation (UVR; up to 24 h) for assessing photochemical reactions in surface waters or in water treatment, respectively. The sweeteners were dissolved in deionised water for examination of direct photochemical reactions. Direct photochemical reactions degraded all sweeteners under UVR but only acesulfame under simulated solar radiation. Acesulfame was degraded over three orders of magnitude faster than the other sweeteners. For examining indirect photochemical reactions, the sweeteners were dissolved in surface waters with indigenous dissolved organic matter or irradiated with aqueous solutions of nitrate (1 mg N/L) and ferric iron (2.8 mg Fe/L) introduced as sensitizers. Iron enhanced the photodegradation rates but nitrate and dissolved organic matter did not. UVR transformed acesulfame into at least three products: iso-acesulfame, hydroxylated acesulfame and hydroxypropanyl sulfate. Photolytic half-life was one year for acesulfame and more than several years for the other sweeteners in surface waters under solar radiation. Our study shows that the photochemical reactivity of commonly used artificial sweeteners is variable: acesulfame may be sensitive to photodegradation in surface waters, while saccharin, cyclamic acid and sucralose degrade very slowly even under the energetic UVR commonly used in water treatment.

  6. Engineering artificial machines from designable DNA materials for biomedical applications. (United States)

    Qi, Hao; Huang, Guoyou; Han, Yulong; Zhang, Xiaohui; Li, Yuhui; Pingguan-Murphy, Belinda; Lu, Tian Jian; Xu, Feng; Wang, Lin


    Deoxyribonucleic acid (DNA) emerges as building bricks for the fabrication of nanostructure with complete artificial architecture and geometry. The amazing ability of DNA in building two- and three-dimensional structures raises the possibility of developing smart nanomachines with versatile controllability for various applications. Here, we overviewed the recent progresses in engineering DNA machines for specific bioengineering and biomedical applications.

  7. Extraction and amplification of nuclear and mitochondrial DNA from ancient and artificially aged bones. (United States)

    von Wurmb-Schwark, Nicole; Harbeck, Michaela; Wiesbrock, Urs; Schroeder, Inge; Ritz-Timme, Stefanie; Oehmichen, Manfred


    An experimental design is presented that simulates an accelerated process of DNA degradation in human bone tissues and thus provides a possibility for a systematic investigation of factors hampering DNA extraction and amplification. Equal sized slices of human femoral bones were incubated in 90 degrees C water for 2 h up to 30 days. DNA was extracted and subjected to a human specific Duplex polymerase chain reaction (PCR) and also to a Multiplex short tandem repeat (STR) PCR. Additionally 24 ancient bones representing different age periods were investigated in the same way. The results were compared to those from the artificially aged samples. After just 12 h of incubation, DNA is totally degraded, but still fully typable. After 36 h no reproducible amplification of DNA is possible. Using Multiplex PCR the DNA from artificially aged bones shows the typical STR pattern for ancient samples suggesting that the in vitro approach provides a useful and comparable method to elucidate the DNA degradation process in bones.

  8. A new sensitive short pentaplex (ShoP) PCR for typing of degraded DNA. (United States)

    Meissner, C; Bruse, P; Mueller, E; Oehmichen, M


    Analysis of short tandem repeat makers has become the most powerful tool for DNA typing in forensic casework analysis. Unfortunately, typing of DNA extracted from telogen shed hairs, bones buried in the soil or from paraffin-embedded, formalin-fixed tissue often reveals no results due to the degradation of DNA. The reduction in size of the target fragments by development of new primers and their combination in multiplex approaches open a new field of DNA analysis. Here we present a new sensitive short pentaplex PCR including the loci amelogenin, TH01, VWA, D3S1358 and D8S1179. Validation tests of our new method included sensitivity, mixtures, human specificity, artificial degradation of DNA by DNase I and case work analysis on a panel of different forensic samples. The detection limit was 12.5 pg of human DNA, and mixtures of 50 pg in a total of 1000 pg were clearly detectable and revealed complete profiles. Only DNA extracts of human primates displayed a few signals, whereas other animal, fungal or bacterial DNA showed no signals. Our method proved extremely valuable in the analysis of artificially degraded DNA and in forensic cases, where only poorly preserved DNA was available. This approach and other similar methods can aid in the analysis of samples where allelic drop out of larger fragments is observed. It is highly recommended to develop more of these multiplexes to improve poor quality DNA typing.

  9. Magnesium degradation as determined by artificial neural networks. (United States)

    Willumeit, Regine; Feyerabend, Frank; Huber, Norbert


    Magnesium degradation under physiological conditions is a highly complex process in which temperature, the use of cell culture growth medium and the presence of CO2, O2 and proteins can influence the corrosion rate and the composition of the resulting corrosion layer. Due to the complexity of this process it is almost impossible to predict the parameters that are most important and whether some parameters have a synergistic effect on the corrosion rate. Artificial neural networks are a mathematical tool that can be used to approximate and analyse non-linear problems with multiple inputs. In this work we present the first analysis of corrosion data obtained using this method, which reveals that CO2 and the composition of the buffer system play a crucial role in the corrosion of magnesium, whereas O2, proteins and temperature play a less prominent role.

  10. Artificial, parallel, left-handed DNA helices. (United States)

    Tian, Cheng; Zhang, Chuan; Li, Xiang; Li, Yingmei; Wang, Guansong; Mao, Chengde


    This communication reports an engineered DNA architecture. It contains multiple domains of half-turn-long, standard B-DNA duplexes. While each helical domain is right-handed and its two component strands are antiparallel, the global architecture is left-handed and the two component DNA strands are oriented parallel to each other.

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

    DEFF Research Database (Denmark)

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


    The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation r...

  12. In vitro DNA binding studies of Aspartame, an artificial sweetener. (United States)

    Kashanian, Soheila; Khodaei, Mohammad Mehdi; Kheirdoosh, Fahimeh


    A number of small molecules bind directly and selectively to DNA, by inhibiting replication, transcription or topoisomerase activity. In this work the interaction of native calf thymus DNA (CT-DNA) with Aspartame (APM), an artificial sweeteners was studied at physiological pH. DNA binding study of APM is useful to understand APM-DNA interaction mechanism and to provide guidance for the application and design of new and safer artificial sweeteners. The interaction was investigated using spectrophotometric, spectrofluorometric competition experiment and circular dichroism (CD). Hypochromism and red shift are shown in UV absorption band of APM. A strong fluorescence quenching reaction of DNA to APM was observed and the binding constants (Kf) of DNA with APM and corresponding number of binding sites (n) were calculated at different temperatures. Thermodynamic parameters, enthalpy changes (ΔH) and entropy changes (ΔS) were calculated to be +181kJmol(-1) and +681Jmol(-1)K(-1) according to Van't Hoff equation, which indicated that reaction is predominantly entropically driven. Moreover, spectrofluorometric competition experiment and circular dichroism (CD) results are indicative of non-intercalative DNA binding nature of APM. We suggest that APM interacts with calf thymus DNA via groove binding mode with an intrinsic binding constant of 5×10(+4)M(-1).

  13. Single-tube library preparation for degraded DNA

    DEFF Research Database (Denmark)

    Carøe, Christian; Gopalakrishnan, Shyam; Vinner, Lasse


    1.In recent years, massive parallel sequencing has revolutionized the study of degraded DNA, thus enabling the field of ancient DNA to evolve into that of paleogenomics. Despite these advances, the recovery and sequencing of degraded DNA remains challenging due to limitations in the manipulation...... of chemically damaged and highly fragmented DNA molecules. In particular, the enzymatic reactions and DNA purification steps during library preparation can result in DNA template loss and sequencing biases, affecting downstream analyses. The development of library preparation methods that circumvent...... these obstacles and enable higher throughput are therefore of interest to researchers working with degraded DNA. 2.In this study, we compare four Illumina library preparation protocols, including two “single-tube” methods developed for this study with the explicit aim of improving data quality and reducing...

  14. Specific incorporation of an artificial nucleotide opposite a mutagenic DNA adduct by a DNA polymerase. (United States)

    Wyss, Laura A; Nilforoushan, Arman; Eichenseher, Fritz; Suter, Ursina; Blatter, Nina; Marx, Andreas; Sturla, Shana J


    The ability to detect DNA modification sites at single base resolution could significantly advance studies regarding DNA adduct levels, which are extremely difficult to determine. Artificial nucleotides that are specifically incorporated opposite a modified DNA site offer a potential strategy for detection of such sites by DNA polymerase-based systems. Here we investigate the action of newly synthesized base-modified benzimidazole-derived 2'-deoxynucleoside-5'-O-triphosphates on DNA polymerases when performing translesion DNA synthesis past the pro-mutagenic DNA adduct O(6)-benzylguanine (O(6)-BnG). We found that a mutated form of KlenTaq DNA polymerase, i.e., KTqM747K, catalyzed O(6)-BnG adduct-specific processing of the artificial BenziTP in favor of the natural dNTPs. Steady-state kinetic parameters revealed that KTqM747K catalysis of BenziTP is 25-fold more efficient for template O(6)-BnG than G, and 5-fold more efficient than natural dTMP misincorporation in adduct bypass. Furthermore, the nucleotide analogue BenziTP is required for full-length product formation in O(6)-BnG bypass, as without BenziTP the polymerase stalls at the adduct site. By combining the KTqM747K polymerase and BenziTP, a first round of DNA synthesis enabled subsequent amplification of Benzi-containing DNA. These results advance the development of technologies for detecting DNA adducts.

  15. Artificial network prediction on degradable properties of coal-filled films

    Institute of Scientific and Technical Information of China (English)

    YANG Zhi-yuan; ZHOU An-ning; QU Jian-lin


    Utilized degradable data of coal-filled films from the accelerated UV chamber ageing degradation experiments, and on the basis of control factors' analysis, presented a predicting model on degradable properties of this film in photo-degradation according to back-propagation artificial neural network (BP ANN). 4 controlling factors in films degradation, including temperature, the time of UV irradiation, the concentration and the type of coals were used as input parameters in the ANN model. While the degradable properties after film degradation, including the mechanical properties and carbonyl index, were used as output parameters. It was carried out by the neural network toolbox of Matlab 6.5 software and Visual Basic 6.0. Discussed partition of sample data and model's parameters,and then selected the best configuration of ANN network. The accurate scope of predicting results was analyzed. This model has a high precision in predicting on properties of the coal-filled film degradation.

  16. Differential cDNA cloning by enzymatic degrading subtraction (EDS).



    We describe a new method, called enzymatic degrading subtraction (EDS), for the construction of subtractive libraries from PCR amplified cDNA. The novel features of this method are that i) the tester DNA is blocked by thionucleotide incorporation; ii) the rate of hybridization is accelerated by phenol-emulsion reassociation; and iii) the driver cDNA and hybrid molecules are enzymatically removed by digestion with exonucleases III and VII rather than by physical partitioning. We demonstrate th...

  17. [DNA degradation during standard alkaline of thermal denaturation]. (United States)

    Drozhdeniuk, A P; Sulimova, G E; Vaniushin, B F


    Essential degradation 8 DNA (up to 10 per cent) with liberation of acid-soluble fragments takes place on the standard alkaline (0,01 M sodium phosphate, pH 12, 60 degrees, 15 min) or thermal (0.06 M sodium phosphate buffer, pH 6.8, 102 degrees C, 15 min) denaturation. This degradation is more or less selective: fraction of low molecular weight fragments, isolated by hydroxyapatite cromatography and eluted by 0.06 M sodium phosphate buffer, pH 6.8 is rich in adenine and thymine and contains about 2 times less 5-methylcytosine than the total wheat germ DNA. The degree of degradation of DNA on thermal denaturation is higher than on alkaline degradation. Therefore while studying reassociation of various DNA, one and the same standard method of DNA denaturation should be used. Besides, both the level of DNA degradation and the nature of the resulting products (fragments) should be taken into account.

  18. Multi-Probe Based Artificial DNA Encoding and Matching Classifier for Hyperspectral Remote Sensing Imagery

    Directory of Open Access Journals (Sweden)

    Ke Wu


    Full Text Available In recent years, a novel matching classification strategy inspired by the artificial deoxyribonucleic acid (DNA technology has been proposed for hyperspectral remote sensing imagery. Such a method can describe brightness and shape information of a spectrum by encoding the spectral curve into a DNA strand, providing a more comprehensive way for spectral similarity comparison. However, it suffers from two problems: data volume is amplified when all of the bands participate in the encoding procedure and full-band comparison degrades the importance of bands carrying key information. In this paper, a new multi-probe based artificial DNA encoding and matching (MADEM method is proposed. In this method, spectral signatures are first transformed into DNA code words with a spectral feature encoding operation. After that, multiple probes for interesting classes are extracted to represent the specific fragments of DNA strands. During the course of spectral matching, the different probes are compared to obtain the similarity of different types of land covers. By computing the absolute vector distance (AVD between different probes of an unclassified spectrum and the typical DNA code words from the database, the class property of each pixel is set as the minimum distance class. The main benefit of this strategy is that the risk of redundant bands can be deeply reduced and critical spectral discrepancies can be enlarged. Two hyperspectral image datasets were tested. Comparing with the other classification methods, the overall accuracy can be improved from 1.22% to 10.09% and 1.19% to 15.87%, respectively. Furthermore, the kappa coefficient can be improved from 2.05% to 15.29% and 1.35% to 19.59%, respectively. This demonstrated that the proposed algorithm outperformed other traditional classification methods.

  19. DNA Profiling Success Rates from Degraded Skeletal Remains in Guatemala. (United States)

    Johnston, Emma; Stephenson, Mishel


    No data are available regarding the success of DNA Short Tandem Repeat (STR) profiling from degraded skeletal remains in Guatemala. Therefore, DNA profiling success rates relating to 2595 skeletons from eleven cases at the Forensic Anthropology Foundation of Guatemala (FAFG) are presented. The typical postmortem interval was 30 years. DNA was extracted from bone powder and amplified using Identifiler and Minifler. DNA profiling success rates differed between cases, ranging from 50.8% to 7.0%, the overall success rate for samples was 36.3%. The best DNA profiling success rates were obtained from femur (36.2%) and tooth (33.7%) samples. DNA profiles were significantly better from lower body bones than upper body bones (p = forensic DNA sampling strategies in future victim recovery investigations.

  20. Post mortem DNA degradation of human tissue experimentally mummified in salt. (United States)

    Shved, Natallia; Haas, Cordula; Papageorgopoulou, Christina; Akguel, Guelfirde; Paulsen, Katja; Bouwman, Abigail; Warinner, Christina; Rühli, Frank


    Mummified human tissues are of great interest in forensics and biomolecular archaeology. The aim of this study was to analyse post mortem DNA alterations in soft tissues in order to improve our knowledge of the patterns of DNA degradation that occur during salt mummification. In this study, the lower limb of a female human donor was amputated within 24 h post mortem and mummified using a process designed to simulate the salt dehydration phase of natural or artificial mummification. Skin and skeletal muscle were sampled at multiple time points over a period of 322 days and subjected to genetic analysis. Patterns of genomic fragmentation, miscoding lesions, and overall DNA degradation in both nuclear and mitochondrial DNA was assessed by different methods: gel electrophoresis, multiplex comparative autosomal STR length amplification, cloning and sequence analysis, and PCR amplification of different fragment sizes using a damage sensitive recombinant polymerase. The study outcome reveals a very good level of DNA preservation in salt mummified tissues over the course of the experiment, with an overall slower rate of DNA fragmentation in skin compared to muscle.

  1. Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing.

    Directory of Open Access Journals (Sweden)

    Longfei Jiang

    Full Text Available Microorganisms responsible for the degradation of phenanthrene in a clean forest soil sample were identified by DNA-based stable isotope probing (SIP. The soil was artificially amended with either 12C- or 13C-labeled phenanthrene, and soil DNA was extracted on days 3, 6 and 9. Terminal restriction fragment length polymorphism (TRFLP results revealed that the fragments of 219- and 241-bp in HaeIII digests were distributed throughout the gradient profile at three different sampling time points, and both fragments were more dominant in the heavy fractions of the samples exposed to the 13C-labeled contaminant. 16S rRNA sequencing of the 13C-enriched fraction suggested that Acidobacterium spp. within the class Acidobacteria, and Collimonas spp. within the class Betaproteobacteria, were directly involved in the uptake and degradation of phenanthrene at different times. To our knowledge, this is the first report that the genus Collimonas has the ability to degrade PAHs. Two PAH-RHDα genes were identified in 13C-labeled DNA. However, isolation of pure cultures indicated that strains of Staphylococcus sp. PHE-3, Pseudomonas sp. PHE-1, and Pseudomonas sp. PHE-2 in the soil had high phenanthrene-degrading ability. This emphasizes the role of a culture-independent method in the functional understanding of microbial communities in situ.

  2. Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples (United States)

    Dong, Chun-nan; Yang, Ya-dong; Li, Shu-jin; Yang, Ya-ran; Zhang, Xiao-jing; Fang, Xiang-dong; Yan, Jiang-wei; Cong, Bin


    In the case of mass disasters, missing persons and forensic caseworks, highly degraded biological samples are often encountered. It can be a challenge to analyze and interpret the DNA profiles from these samples. Here we provide a new strategy to solve the problem by taking advantage of the intrinsic structural properties of DNA. We have assessed the in vivo positions of more than 35 million putative nucleosome cores in human leukocytes using high-throughput whole genome sequencing, and identified 2,462 single nucleotide variations (SNVs), 128 insertion-deletion polymorphisms (indels). After comparing the sequence reads with 44 STR loci commonly used in forensics, five STRs (TH01, TPOX, D18S51, DYS391, and D10S1248)were matched. We compared these “nucleosome protected STRs” (NPSTRs) with five other non-NPSTRs using mini-STR primer design, real-time PCR, and capillary gel electrophoresis on artificially degraded DNA. Moreover, genotyping performance of the five NPSTRs and five non-NPSTRs was also tested with real casework samples. All results show that loci located in nucleosomes are more likely to be successfully genotyped in degraded samples. In conclusion, after further strict validation, these markers could be incorporated into future forensic and paleontology identification kits, resulting in higher discriminatory power for certain degraded sample types. PMID:27189082

  3. Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq). (United States)

    Graham, Carly F; Glenn, Travis C; McArthur, Andrew G; Boreham, Douglas R; Kieran, Troy; Lance, Stacey; Manzon, Richard G; Martino, Jessica A; Pierson, Todd; Rogers, Sean M; Wilson, Joanna Y; Somers, Christopher M


    Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double-digest RADSeq approach (3RAD). We generated libraries using genomic DNA serially extracted from the muscle tissue of 8 individual lake whitefish (Coregonus clupeaformis) following 0-, 12-, 48- and 96-h incubation at room temperature posteuthanasia. This treatment of the tissue resulted in input DNA that ranged in quality from nearly intact to highly sheared. All samples were sequenced as a multiplexed pool on an Illumina MiSeq. Libraries created from low to moderately degraded DNA (12-48 h) performed well. In contrast, the number of RADtags per individual, number of variable sites, and percentage of identical RADtags retained were all dramatically reduced when libraries were made using highly degraded DNA (96-h group). This reduction in performance was largely due to a significant and unexpected loss of raw reads as a result of poor quality scores. Our findings remained consistent after changes in restriction enzymes, modified fold coverage values (2- to 16-fold), and additional read-length trimming. We conclude that starting DNA quality is an important consideration for RADSeq; however, the approach remains robust until genomic DNA is extensively degraded.

  4. Artificial ants deposit pheromone to search for regulatory DNA elements

    Directory of Open Access Journals (Sweden)

    Liu Yunlong


    Full Text Available Abstract Background Identification of transcription-factor binding motifs (DNA sequences can be formulated as a combinatorial problem, where an efficient algorithm is indispensable to predict the role of multiple binding motifs. An ant algorithm is a biology-inspired computational technique, through which a combinatorial problem is solved by mimicking the behavior of social insects such as ants. We developed a unique version of ant algorithms to select a set of binding motifs by considering a potential contribution of each of all random DNA sequences of 4- to 7-bp in length. Results Human chondrogenesis was used as a model system. The results revealed that the ant algorithm was able to identify biologically known binding motifs in chondrogenesis such as AP-1, NFκB, and sox9. Some of the predicted motifs were identical to those previously derived with the genetic algorithm. Unlike the genetic algorithm, however, the ant algorithm was able to evaluate a contribution of individual binding motifs as a spectrum of distributed information and predict core consensus motifs from a wider DNA pool. Conclusion The ant algorithm offers an efficient, reproducible procedure to predict a role of individual transcription-factor binding motifs using a unique definition of artificial ants.

  5. Organic coatings degradation: Comparison between natural and artificial weathering

    Energy Technology Data Exchange (ETDEWEB)

    Deflorian, F. [Department of Materials Engineering and Industrial Technologies, University of Trento, Via Mesiano 77, Trento (Italy)], E-mail:; Rossi, S.; Fedel, M. [Department of Materials Engineering and Industrial Technologies, University of Trento, Via Mesiano 77, Trento (Italy)


    The protective properties of organic coated galvanised steel for outdoor applications are generally evaluated by means of accelerated laboratory tests, including electrochemical techniques. An open question is how these accelerated tests can be correlated with natural exposure in different environments. It is well known that many papers did not found any significant correlation between the natural exposure and laboratory tests. In this paper we propose a different approach. The starting point is the consideration to define the natural weathering by monitoring a few different environmental parameters affecting the organic coatings properties (energy from UV radiation, wet time, temperature, etc.), and not just considering the time of exposure. We studied two different galvanised materials: Zn and Zn-Al coatings, three different primers and one top coat. The samples were exposed for 12 months in three different natural environments: Trento (Italy), alpine region, Marseille (France) by the Mediterranean sea and Daytona (USA), a humid tropical environment. At the same time all the meteorological parameters were collected. The coatings weathering was evaluated in the laboratory after some different accelerated tests (salt spray chamber, UV exposure, cyclic test) and after natural exposure. A correlation between the 'natural stresses' and the 'artificial stresses' was investigated.

  6. Bacterial DNA Sequence Compression Models Using Artificial Neural Networks

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    Armando J. Pinho


    Full Text Available It is widely accepted that the advances in DNA sequencing techniques have contributed to an unprecedented growth of genomic data. This fact has increased the interest in DNA compression, not only from the information theory and biology points of view, but also from a practical perspective, since such sequences require storage resources. Several compression methods exist, and particularly, those using finite-context models (FCMs have received increasing attention, as they have been proven to effectively compress DNA sequences with low bits-per-base, as well as low encoding/decoding time-per-base. However, the amount of run-time memory required to store high-order finite-context models may become impractical, since a context-order as low as 16 requires a maximum of 17.2 x 109 memory entries. This paper presents a method to reduce such a memory requirement by using a novel application of artificial neural networks (ANN to build such probabilistic models in a compact way and shows how to use them to estimate the probabilities. Such a system was implemented, and its performance compared against state-of-the art compressors, such as XM-DNA (expert model and FCM-Mx (mixture of finite-context models , as well as with general-purpose compressors. Using a combination of order-10 FCM and ANN, similar encoding results to those of FCM, up to order-16, are obtained using only 17 megabytes of memory, whereas the latter, even employing hash-tables, uses several hundreds of megabytes.

  7. Investigation of the In Vitro Degradation of a Novel Polylactide/Nanohydroxyapatite Composite for Artificial Bone

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    Jianghong Huang


    Full Text Available We prepared the poly-L-lactic acid (PLLA/nanohydroxyapatite (n-HA composite and investigated the in vitro degradation of pure PLLA material and PLLA/n-HA composites in order to identify a suitable and ideal artificial bone tissue repair material. The water uptake, weight loss, and changes in the PBS pH value and in the mechanical properties of material were measured during the processes that PLLA and PLLA/n-HA biological composites were degraded in PBS. We also performed electron microscopic scanning of the material fracture surface and observed the microscopic morphologies of materials during the degradation process. We found that the degradation rate of the PLLA/n-HA material was slower than the PLLA material, and there was a little degradation of the PLLA/n-HA material at early stages. The PLLA/n-HA material also maintained the initial mechanical strength better than the pure PLLA material. The PLLA/n-HA material is thus a better material for artificial bone than the pure PLLA material.

  8. Artificial Solid Electrolyte Interphase to Address the Electrochemical Degradation of Silicon Electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Dudney, Nancy J [ORNL; Nanda, Jagjit [ORNL; Liang, Chengdu [ORNL; Li, Juchuan [ORNL


    Electrochemical degradation on Si anodes prevents them from being successfully used in lithium-ion full cells. Unlike the case of graphite anodes, natural solid electrolyte interphase (SEI) films generated from carbonate electrolyte do not self-passivate on Si and causes continuous electrolyte decomposition. In this work we aim at solving the issue of electrochemical degradation by fabricating artificial SEI films using a solid electrolyte material, lithium phosphor oxynitride (Lipon), that conducts Li ions and blocks electrons. For Si anodes coated with Lipon of 50 nm or thicker, significant effect is observed in suppressing the electrolyte decomposition, while Lipon of thinner than 40 nm has little effect. Ionic and electronic conductivity measurement reveals that the artificial SEI is effective when it is a pure ionic conductor, and the electrolyte decomposition is not suppressed when the artificial SEI is a mixed electronic-ionic conductor. The critical thickness for this transition in conducting behavior is found to be 40~50 nm. This work provides guidance for designing artificial SEI for high capacity lithium-ion battery electrodes using solid electrolyte materials.

  9. DNase I induced DNA degradation is inhibited by neomycin. (United States)

    Woegerbauer, M; Burgmann, H; Davies, J; Graninger, W


    Preparations of antimicrobials from biotechnological sources containing nucleic acids may serve as vector for the dissemination of resistance genes. An essential prerequisite for the acquisition of a new resistance phenotype in a transformational scenario is the availability of physically intact DNA molecules capable of transforming competent microorganisms. DNA is thought to be an easy target for catabolic processes when present in the natural habitat of bacteria (e.g. gastrointestinal tract, soil) due to the overall presence of nucleolytic enzymes. Aminoglycoside antibiotics are known to display a strong affinity to nucleic acids rendering these compounds to be primary candidates for exerting DNA protective functions in the gastrointestinal tract when applied orally during antibiotic chemotherapy. Using a DNase I protection assay it could be demonstrated that neomycin B at a concentration of 2 mM completely inhibited degradation of plasmid DNA in vitro. No inhibition of degradation was observed with streptomycin and kanamycin and the non-aminoglycoside antibiotics oxytetracycline and ampicillin under identical assay conditions. Thus, neomycin preparations may be able to promote structural integrity of contaminating DNA-fragments in DNase-rich environments.

  10. Design of artificial nucleases and studies of their interaction with DNA

    Institute of Scientific and Technical Information of China (English)

    ZHANG JingJing; SHAO Ying; WEI Li; LI Ying; SHENG Xin; LIU Fang; LU GuoYuan


    The design of artificial nucleases and nuclease mimics has attracted extensive attention and made great progress due to their significant scientific meanings and potential application in the field of gene medicine and molecular biology. This paper reviews recent progress in the investigation of artificial nuclease, including "bifunctional cooperative catalysis", "dinuclear synergistic catalysis", "metal-free catalysis", and especially, the studies of aza-crown ethers as artificial nucleases and their interaction with DNA.

  11. Design of artificial nucleases and studies of their interaction with DNA

    Institute of Scientific and Technical Information of China (English)


    The design of artificial nucleases and nuclease mimics has attracted extensive attention and made great progress due to their significant scientific meanings and potential application in the field of gene medicine and molecular biology. This paper reviews recent progress in the investigation of artificial nuclease,including "bifunctional cooperative catalysis","dinuclear synergistic catalysis","metal-free catalysis" ,and especially,the studies of aza-crown ethers as artificial nucleases and their interaction with DNA.

  12. Degradable starch nanoparticle assisted ethanol precipitation of DNA. (United States)

    Ip, Alexander C-F; Tsai, Tsung Hao; Khimji, Imran; Huang, Po-Jung Jimmy; Liu, Juewen


    Precipitation of DNA from a large volume of aqueous solution is an important step in many molecular biology and analytical chemistry experiments. Currently, this is mainly achieved by ethanol precipitation, where a long-term incubation (usually overnight) at low temperature of -20 to -80°C with high salt concentration is required. This method also requires a large quantity of DNA to form a visible pellet and was tested mainly for double-stranded DNA. To improve DNA precipitation, co-precipitating polymers such as linear polyacrylamide has been used. In this work, we report that starch nanoparticles (SNPs) can achieve convenient DNA precipitation at room temperature with a low salt concentration and short incubation time. This method requires as low as 0.01-0.1% SNPs and can precipitate both single- and double-stranded DNA of various lengths. The effect of salt concentration, pH and the crosslinking density of SNPs has been systematically studied. Compared to other types of precipitating agents, SNPs are highly biocompatible and can be degraded by a common enzyme (amylase). This work suggests a novel application of a bio-based material that is prepared in mass production.

  13. Artificial Metalloenzymes for Asymmetric Catalysis by Creation of Novel Active Sites in Protein and DNA Scaffolds

    NARCIS (Netherlands)

    Drienovska, Ivana; Roelfes, Gerard


    Artificial metalloenzymes have emerged as a promising new approach to asymmetric catalysis. In our group, we are exploring novel artificial metalloenzyme designs involving creation of a new active site in a protein or DNA scaffold that does not have an existing binding pocket. In this review, we giv

  14. Nuclear fragmentation and DNA degradation during programmed cell death in petals of morning glory (Ipomoea nil)

    NARCIS (Netherlands)

    Yamada, T.; Takatsu, Y.; Kasumi, K.; Ichimura, K.; Doorn, van W.G.


    We studied DNA degradation and nuclear fragmentation during programmed cell death (PCD) in petals of Ipomoea nil (L.) Roth flowers. The DNA degradation, as observed on agarose gels, showed a large increase. Using DAPI, which stains DNA, and flow cytometry for DAPI fluorescence, we found that the num

  15. Nuclear fragmentation and DNA degradation during programmed cell death in petals of morning glory (Ipomoea nil)

    NARCIS (Netherlands)

    Yamada, T.; Takatsu, Y.; Kasumi, K.; Ichimura, K.; Doorn, van W.G.


    We studied DNA degradation and nuclear fragmentation during programmed cell death (PCD) in petals of Ipomoea nil (L.) Roth flowers. The DNA degradation, as observed on agarose gels, showed a large increase. Using DAPI, which stains DNA, and flow cytometry for DAPI fluorescence, we found that the

  16. Degradation and mineralization of phenol compounds with goethite catalyst and mineralization prediction using artificial intelligence. (United States)

    Tisa, Farhana; Davoody, Meysam; Abdul Raman, Abdul Aziz; Daud, Wan Mohd Ashri Wan


    The efficiency of phenol degradation via Fenton reaction using mixture of heterogeneous goethite catalyst with homogeneous ferrous ion was analyzed as a function of three independent variables, initial concentration of phenol (60 to 100 mg /L), weight ratio of initial concentration of phenol to that of H2O2 (1: 6 to 1: 14) and, weight ratio of initial concentration of goethite catalyst to that of H2O2 (1: 0.3 to 1: 0.7). More than 90 % of phenol removal and more than 40% of TOC removal were achieved within 60 minutes of reaction. Two separate models were developed using artificial neural networks to predict degradation percentage by a combination of Fe3+ and Fe2+ catalyst. Five operational parameters were employed as inputs while phenol degradation and TOC removal were considered as outputs of the developed models. Satisfactory agreement was observed between testing data and the predicted values (R2Phenol = 0.9214 and R2TOC= 0.9082).

  17. MiniSTR multiplex systems based on non-CODIS loci for analysis of degraded DNA samples. (United States)

    Asamura, H; Fujimori, S; Ota, M; Fukushima, H


    We describe two short amplicon autosomal short tandem repeat (miniSTR) quadruplex systems for eight loci D1S1171, D2S1242, D3S1545, D4S2366, D12S391, D16S3253, D20S161, and D21S1437, unlinked from the combined DNA index system (non-CODIS) loci, using newly designed primer sets. The results of an assay of 411 Japanese individuals showed that polymerase chain reaction (PCR) products within the eight loci were less than 150bp in size, without the seven additional bases for adenylation. The frequency distributions in the loci showed no deviations from Hardy-Weinberg equilibrium expectations. The accumulated power of discrimination and power of exclusion for the eight loci were 0.9999999991 and 0.998, respectively. For assay of highly degraded DNA, including artificially degraded samples and the degraded forensic casework samples assessed with the present miniSTR quadruplex systems, the systems proved quite effective in analyzing degraded DNA.

  18. Degradation and antibacterial properties of magnesium alloys in artificial urine for potential resorbable ureteral stent applications. (United States)

    Lock, Jaclyn Y; Wyatt, Eric; Upadhyayula, Srigokul; Whall, Andrew; Nuñez, Vicente; Vullev, Valentine I; Liu, Huinan


    This article presents an investigation on the effectiveness of magnesium and its alloys as a novel class of antibacterial and biodegradable materials for ureteral stent applications. Magnesium is a lightweight and biodegradable metallic material with beneficial properties for use in medical devices. Ureteral stent is one such example of a medical device that is widely used to treat ureteral canal blockages clinically. The bacterial colony formation coupled with the encrustation on the stent surface from extended use often leads to clinical complications and contributes to the failure of indwelling medical devices. We demonstrated that magnesium alloys decreased Escherichia coli viability and reduced the colony forming units over a 3-day incubation period in an artificial urine (AU) solution when compared with currently used commercial polyurethane stent. Moreover, the magnesium degradation resulted in alkaline pH and increased magnesium ion concentration in the AU solution. The antibacterial and degradation properties support the potential use of magnesium-based materials for next-generation ureteral stents. Further studies are needed for clinical translation of biodegradable metallic ureteral stents.

  19. Construction of two fluorescence-labeled non-combined DNA index system miniSTR multiplex systems to analyze degraded DNA samples in the Chinese Han Population. (United States)

    Bai, Xue; Li, Shujin; Cong, Bin; Li, Xia; Guo, Xia; He, Lujun; Ye, Jian; Pei, Li


    MiniSTR loci have been demonstrated to be an effective approach in recovering genetic information from degraded specimens, because of the reduced PCR amplicon sizes which improved the PCR efficiency. Eight non-combined DNA index system miniSTR loci suitable for the Chinese Han Population were analyzed in 300 unrelated Chinese Han individuals using two novel five fluorescence-labeled miniSTR multiplex systems(multiplex I: D10S1248, D2S441, D1S1677 and D9S2157; multiplex II: D9S1122, D10S1435, D12ATA63, D2S1776 and Amelogenin). The allele frequency distribution and forensic parameters in the Chinese Han Population were reported in this article. The Exact Test demonstrated that all loci surveyed here were found to be no deviation from Hardy-Weinberg equilibrium. The accumulated power of discrimination and power of exclusion for the eight loci were 0.999999992 and 0.98, respectively. The highly degraded DNA from artificially degraded samples and the degraded forensic case work samples was assessed with the two miniSTR multiplex systems, and the results showed that the systems were quite effective.

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

    Directory of Open Access Journals (Sweden)

    Gamal. F. Elhadi


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

  1. Genetic diversity analysis of mitochondrial DNA control region in artificially propagated Chinese sucker Myxocyprinus asiaticus. (United States)

    Wan, Yuan; Zhou, Chun-Hua; Ouyang, Shan; Huang, Xiao-Chen; Zhan, Yang; Zhou, Ping; Rong, Jun; Wu, Xiao-Ping


    The genetic diversity of the three major artificially propagated populations of Chinese sucker, an endangered freshwater fish species, was investigated using the sequences of mitochondrial DNA (mtDNA) control regions. Among the 89 individuals tested, 66 variable sites (7.26%) and 10 haplotypes were detected (Haplotype diversity Hd = 0.805, Nucleotide diversity π = 0.0287). In general, genetic diversity was lower in artificially propagated populations than in wild populations. This reduction in genetic diversity may be due to population bottlenecks, genetic drift and human selection. A stepping-stone pattern of gene flow was detected in the populations studied, showing much higher gene flow between neighbouring populations. To increase the genetic diversity, wild lineages should be introduced, and more lineages should be shared among artificially propagated populations.

  2. AISMOTIF-An Artificial Immune System for DNA Motif Discovery

    CERN Document Server

    Seeja, K R


    Discovery of transcription factor binding sites is a much explored and still exploring area of research in functional genomics. Many computational tools have been developed for finding motifs and each of them has their own advantages as well as disadvantages. Most of these algorithms need prior knowledge about the data to construct background models. However there is not a single technique that can be considered as best for finding regulatory motifs. This paper proposes an artificial immune system based algorithm for finding the transcription factor binding sites or motifs and two new weighted scores for motif evaluation. The algorithm is enumerative, but sufficient pruning of the pattern search space has been incorporated using immune system concepts. The performance of AISMOTIF has been evaluated by comparing it with eight state of art composite motif discovery algorithms and found that AISMOTIF predicts known motifs as well as new motifs from the benchmark dataset without any prior knowledge about the data...

  3. Preparation of high molecular weight gDNA and bacterial artificial chromosome (BAC) libraries in plants. (United States)

    Biradar, Siddanagouda S; Nie, Xiaojun; Feng, Kewei; Weining, Song


    Bacterial artificial chromosome (BAC) libraries are extremely valuable large-insert DNA libraries for physical mapping, positional cloning, comparative genomic analysis, complete genome sequencing, and evolutionary studies. Due to their stability and relative simplicity BAC libraries are most preferred over other approaches for cloning large genomic DNA fragments for large-insert libraries. Isolation of intact high molecular weight (HMW) DNA is a critical step underlying the success of large-insert genomic DNA library construction. It requires the isolation of purified nuclei, embedding them into LMP agarose plugs, restriction digestion of the plugs, and quite often size selection using PFGE and electro-elution of insert DNA. The construction of BAC libraries is complex and challenging for most molecular laboratories. To facilitate the construction of BAC libraries, we present a step-by-step protocol for isolation of HMW DNA and construction of plant BAC libraries.

  4. Determination of type and concentration of DNA nitrogenous bases by Raman spectroscopy using artificial neural networks (United States)

    Laptinskiy, Kirill A.; Burikov, Sergey A.; Sarmanova, Olga E.; Dolenko, Sergey A.; Dolenko, Tatiana A.


    In this article the results of solution of two-parametrical inverse problems of laser Raman spectroscopy of identification and determination of concentration of DNA nitrogenous bases in two-component solutions are presented. Elaboration of methods of control of reactions with DNA strands in remote real-time mode is necessary for solution of one of the basic problems of creation of biocomputers - increase of reliability of molecular DNA-computations. The comparative analysis of two used methods of solution of stated problems has demonstrated convincing advantages of technique of artificial neural networks. Use of artificial neural networks allowed to reach the accuracy of determination of concentration of each base in two-component solutions 0.2-0.3 g/l.

  5. Statistical model for degraded DNA samples and adjusted probabilities for allelic drop-out

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt;


    Abstract DNA samples found at a scene of crime or obtained from the debris of a mass disaster accident are often subject to degradation. When using the STR DNA technology, the DNA profile is observed via a so-called electropherogram (EPG), where the alleles are identified as signal peaks above a ...

  6. All-or-Nothing Character of DNA Degradation in Bacteria after Ionizing Radiation (United States)

    Pollard, Ernest C.; Kraus, Kathryn


    The response of single cells of Escherichia coli Bs-11 and 15JG151 to radiation-induced DNA degradation has been observed by autoradiography. For both cells it is concluded that the event which causes DNA degradation is of an all-or-nothing character. The unit which suffers degradation is not the whole cell, but each cell has between two and four such units. The results suggest that there is some resynthesis of degraded DNA. Evidence that this occurs is shown by examining the degradation of mass cultures of 15TAU/t3 and t7 below and above the permissive temperature for DNA synthesis. The results on the all-or-nothing character are in agreement with previous studies made by completely different techniques. PMID:4572361

  7. Artificial intelligence approach in analysis of DNA sequences. (United States)

    Brézillon, P J; Zaraté, P; Saci, F


    We present an approach for designing a knowledge-based system, called Sequence Acquisition In Context (SAIC), that will be able to cooperate with a biologist in the analysis of DNA sequences. The main task of the system is the acquisition of the expert knowledge that the biologist uses for solving ambiguities from gel autoradiograms, with the aim of re-using it later for solving similar ambiguities. The various types of expert knowledge constitute what we call the contextual knowledge of the sequence analysis. Contextual knowledge deals with the unavoidable problems that are common in the study of the living material (eg noise on data, difficulties of observations). Indeed, the analysis of DNA sequences from autoradiograms belongs to an emerging and promising area of investigation, namely reasoning with images. The SAIC project is developed in a theoretical framework that is shared with other applications. Not all tasks have the same importance in each application. We use this observation for designing an intelligent assistant system with three applications. In the SAIC project, we focus on knowledge acquisition, human-computer interaction and explanation. The project will benefit research in the two other applications. We also discuss our SAIC project in the context of large international projects that aim to re-use and share knowledge in a repository.

  8. Statistical model for degraded DNA samples and adjusted probabilities for allelic drop-out

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt


    -outs. In this paper, we present a method for measuring the degree of degradation of a sample and demonstrate how to incorporate this in estimating the probability of allelic drop-out. This is done by extending an existing method derived for non-degraded samples. The performance of the methodology is evaluated using......DNA samples found at a scene of crime or obtained from the debris of a mass disaster accident are often subject to degradation. When using the STR DNA technology, the DNA profile is observed via a so-called electropherogram (EPG), where the alleles are identified as signal peaks above a certain...

  9. Effect of food processing on plant DNA degradation and PCR-based GMO analysis: a review. (United States)

    Gryson, Nicolas


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

  10. DNA-mediated self-assembly of artificial vesicles.

    Directory of Open Access Journals (Sweden)

    Maik Hadorn

    Full Text Available BACKGROUND: Although multicompartment systems made of single unilamellar vesicles offer the potential to outperform single compartment systems widely used in analytic, synthetic, and medical applications, their use has remained marginal to date. On the one hand, this can be attributed to the binary character of the majority of the current tethering protocols that impedes the implementation of real multicomponent or multifunctional systems. On the other hand, the few tethering protocols theoretically providing multicompartment systems composed of several distinct vesicle populations suffer from the readjustment of the vesicle formation procedure as well as from the loss of specificity of the linking mechanism over time. METHODOLOGY/PRINCIPAL FINDINGS: In previous studies, we presented implementations of multicompartment systems and resolved the readjustment of the vesicle formation procedure as well as the loss of specificity by using linkers consisting of biotinylated DNA single strands that were anchored to phospholipid-grafted biotinylated PEG tethers via streptavidin as a connector. The systematic analysis presented herein provides evidences for the incorporation of phospholipid-grafted biotinylated PEG tethers to the vesicle membrane during vesicle formation, providing specific anchoring sites for the streptavidin loading of the vesicle membrane. Furthermore, DNA-mediated vesicle-vesicle self-assembly was found to be sequence-dependent and to depend on the presence of monovalent salts. CONCLUSIONS/SIGNIFICANCE: This study provides a solid basis for the implementation of multi-vesicle assemblies that may affect at least three distinct domains. (i Analysis. Starting with a minimal system, the complexity of a bottom-up system is increased gradually facilitating the understanding of the components and their interaction. (ii Synthesis. Consecutive reactions may be implemented in networks of vesicles that outperform current single compartment

  11. Design and Construction of a One-Dimensional DNA Track for an Artificial Molecular Motor

    Directory of Open Access Journals (Sweden)

    Suzana Kovacic


    Full Text Available DNA is a versatile heteropolymer that shows great potential as a building block for a diverse array of nanostructures. We present here a solution to the problem of designing and synthesizing a DNA-based nanostructure that will serve as the track along which an artificial molecular motor processes. This one-dimensional DNA track exhibits periodically repeating elements that provide specific binding sites for the molecular motor. Besides these binding elements, additional sequences are necessary to label specific regions within the DNA track and to facilitate track construction. Designing an ideal DNA track sequence presents a particular challenge because of the many variable elements that greatly expand the number of potential sequences from which the ideal sequence must be chosen. In order to find a suitable DNA sequence, we have adapted a genetic algorithm which is well suited for a large but sparse search space. This algorithm readily identifies long DNA sequences that include all the necessary elements to both facilitate DNA track construction and to present appropriate binding sites for the molecular motor. We have successfully experimentally incorporated the sequence identified by the algorithm into a long DNA track meeting the criteria for observation of the molecular motor's activity.

  12. Human identification & forensic analyses of degraded or low level DNA

    NARCIS (Netherlands)

    Westen, Antoinette-Andrea


    DNA-based human identification is employed in varying situations, such as disaster victim identification, relationship testing and forensic analyses. When DNA is of low quality and/or quantity, standard methods for DNA profiling may not suffice. The research described in this thesis is aimed at the

  13. Human identification & forensic analyses of degraded or low level DNA

    NARCIS (Netherlands)

    Westen, Antoinette-Andrea


    DNA-based human identification is employed in varying situations, such as disaster victim identification, relationship testing and forensic analyses. When DNA is of low quality and/or quantity, standard methods for DNA profiling may not suffice. The research described in this thesis is aimed at the

  14. [Correlation between PMI and DNA degradation of costicartilage and dental pulp cells in human being]. (United States)

    Long, Ren; Wang, Wei-ping; Xiong, Ping


    To probe the correlation between the postmortem interval (PMI) and the DNA degradation of costicartilage and dental pulp cells in human being after death, and to seek a new method for estimating PMI. The image cytometry was used to measure the DNA degradation under different ambient temperatures (30-35 degrees C, 15-20 degrees C) in 0-15 days after death. The average DNA content of two kinds of tissue was degradated with the prolongation of PMI. But there was a plateau period of 0-4 days for dental pulp cells of human being in 15-20 degrees C. There was a high negative correlativity PPMI. PMI could be estimated accurately according to the DNA degradation of costicartilage and dental pulp cells in human being after death.

  15. Studies on a Novel Minor-groove Targeting Artificial Nuclease: Synthesis and DNA Binding Behavior

    Institute of Scientific and Technical Information of China (English)


    Nucleases play an important role in molecular biology, for example, in DNA sequencing. Synthetic polyamide conjugates can be considered as a novel tool for the selective inhibition of gene expressions and also as potential drugs in anticancer or antiviral chemotherapy. In this article, the synthesis of a novel minor-groove targeting artificial nuclease, an oligopyrrol-containing compound, has been reported. It was found that this novel compound can bind DNA in AT-rich minor groove with high affinity and site specificity. DNA binding behavior was determined by using UV-Vis and CD. It is indicated that compound 6 can enhance the Tm of DNA from 80. 4 C to 84. 4 ℃ and that it possesses a high binding constant value(Kb = 3.05×104 L/mol).

  16. Studies of interaction between a new synthesized minor-groove targeting artificial nuclease and DNA (United States)

    Yin, Qiang; Zhang, Zhen; Zhao, Yu-Fen


    Nuclease plays an important role in molecular biology, such as DNA sequencing. Synthetic polyamide conjugates can be considered as new tool in the selective inhibition of gene expression and as potential drugs in anticancer or antiviral chemotherapy. In this paper, a new synthesized minor-groove targeting artificial nuclease, oligopyrrol-containing peptide, was reported. It was found that this new compound can bind DNA in AT-riched minor groove with high affinity and site specificity. DNA binding behavior was determined by UV-vis and circular dichroism (CD) methods. It was indicated that compound 6 can enhance the Tm of oligomer DNA from 51.8 to 63.5 °C and possesses large binding constant ( Kb = 8.83 × 10 4 L/mol).

  17. The genotoxic effects of DNA lesions induced by artificial UV-radiation and sunlight. (United States)

    Schuch, André Passaglia; Menck, Carlos Frederico Martins


    Solar radiation sustains and affects all life forms on Earth. The increase in solar UV-radiation at environmental levels, due to depletion of the stratospheric ozone layer, highlights serious issues of social concern. This becomes still more dramatic in tropical and subtropical regions where radiation-intensity is still higher. Thus, there is the need to evaluate the harmful effects of solar UV-radiation on the DNA molecule as a basis for assessing the risks involved for human health, biological productivity and ecosystems. In order to evaluate the profile of DNA damage induced by this form of radiation and its genotoxic effects, plasmid DNA samples were exposed to artificial-UV lamps and directly to sunlight. The induction of cyclobutane pyrimidine dimer photoproducts (CPDs) and oxidative DNA damage in these molecules were evaluated by means of specific DNA repair enzymes. On the other hand, the biological effects of such lesions were determined through the analysis of the DNA inactivation rate and mutation frequency, after replication of the damaged pCMUT vector in an Escherichia coliMBL50 strain. The results indicated the induction of a significant number of CPDs after exposure to increasing doses of UVC, UVB, UVA radiation and sunlight. Interestingly, these photoproducts are those lesions that better correlate with plasmid inactivation as well as mutagenesis, and the oxidative DNA damages induced present very low correlation with these effects. The results indicated that DNA photoproducts play the main role in the induction of genotoxic effects by artificial UV-radiation sources and sunlight.

  18. Delineating Rearrangements in Single Yeast Artificial Chromosomes by Quantitative DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz-Ulrich G.; Greulich-Bode, Karin M.; Wu, Jenny; Duell, Thomas


    Cloning of large chunks of human genomic DNA in recombinant systems such as yeast or bacterial artificial chromosomes has greatly facilitated the construction of physical maps, the positional cloning of disease genes or the preparation of patient-specific DNA probes for diagnostic purposes. For this process to work efficiently, the DNA cloning process and subsequent clone propagation need to maintain stable inserts that are neither deleted nor otherwise rearranged. Some regions of the human genome; however, appear to have a higher propensity than others to rearrange in any host system. Thus, techniques to detect and accurately characterize such rearrangements need to be developed. We developed a technique termed 'Quantitative DNA Fiber Mapping (QDFM)' that allows accurate tagging of sequence elements of interest with near kilobase accuracy and optimized it for delineation of rearrangements in recombinant DNA clones. This paper demonstrates the power of this microscopic approach by investigating YAC rearrangements. In our examples, high-resolution physical maps for regions within the immunoglobulin lambda variant gene cluster were constructed for three different YAC clones carrying deletions of 95 kb and more. Rearrangements within YACs could be demonstrated unambiguously by pairwise mapping of cosmids along YAC DNA molecules. When coverage by YAC clones was not available, distances between cosmid clones were estimated by hybridization of cosmids onto DNA fibers prepared from human genomic DNA. In addition, the QDFM technology provides essential information about clone stability facilitating closure of the maps of the human genome as well as those of model organisms.

  19. Localized degradation of foreign DNA strands in cells: Only excising the first nucleotide of 5' region. (United States)

    Li, Hui; Shen, Wei; Lam, Michael Hon-Wah; Liang, Haojun


    Intracellular delivery of foreign DNA probes sharply increases the efficiency of various biodetection protocols. Spherical nucleic acid (SNA) conjugate is a new type of probe that consists of a dense oligonucleotide shell attached typically to a gold nanoparticle core. They are widely used as novel labels for in vitro biodetection and intracellular assay. However, the degradation of foreign DNA still remains a challenge that can cause significant signal leakage (false positive signal). Hence, the site and behavior of intracellular degradation need to be investigated. Herein, we discover a localized degradation behavior that only excises the first nucleotide of 5' terminal from a DNA strand, whereas the residual portion of this strand is unbroken in MCF-7 cell. This novel degradation action totally differs from previous opinion that foreign DNA strand would be digested into tiny fragments or even individual nucleotides in cellular environment. On the basis of these findings, we propose a simple and effective way to avoid degradation-caused false positive that one can bypass the degradable site and choose a secure region to label fluorophore along the DNA stand, when using DNA probes for intracellular biodetection. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Artificial modulation of the gating behavior of a K+ channel in a KvAP-DNA chimera.

    Directory of Open Access Journals (Sweden)

    Andrew Wang

    Full Text Available We present experiments where the gating behavior of a voltage-gated ion channel is modulated by artificial ligand binding. We construct a channel-DNA chimera with the KvAP potassium channel reconstituted in an artificial membrane. The channel is functional and the single channel ion conductivity unperturbed by the presence of the DNA. However, the channel opening probability vs. bias voltage, i.e., the gating, can be shifted considerably by the electrostatic force between the charges on the DNA and the voltage sensing domain of the protein. Different hybridization states of the chimera DNA thus lead to different response curves of the channel.

  1. Exonuclease VII is involved in "reckless" DNA degradation in UV-irradiated Escherichia coli. (United States)

    Repar, Jelena; Briški, Nina; Buljubašić, Maja; Zahradka, Ksenija; Zahradka, Davor


    The recA mutants of Escherichia coli exhibit an abnormal DNA degradation that starts at sites of double-strand DNA breaks (DSBs), and is mediated by RecBCD exonuclease (ExoV). This "reckless" DNA degradation occurs spontaneously in exponentially growing recA cells, and is stimulated by DNA-damaging agents. We have previously found that the xonA and sbcD mutations, which inactivate exonuclease I (ExoI) and SbcCD nuclease, respectively, markedly suppress "reckless" DNA degradation in UV-irradiated recA cells. In the present work, we show that inactivation of exonuclease VII (ExoVII) by an xseA mutation contributes to attenuation of DNA degradation in UV-irradiated recA mutants. The xseA mutation itself has only a weak effect, however, it acts synergistically with the xonA or sbcD mutations in suppressing "reckless" DNA degradation. The quadruple xseA xonA sbcD recA mutants show no sign of DNA degradation during post-irradiation incubation, suggesting that ExoVII, together with ExoI and SbcCD, plays a crucial role in regulating RecBCD-catalyzed chromosome degradation. We propose that these nucleases act on DSBs to create blunt DNA ends, the preferred substrates for the RecBCD enzyme. In addition, our results show that in UV-irradiated recF recA(+) cells, the xseA, xonA, and sbcD mutations do not affect RecBCD-mediated DNA repair, suggesting that ExoVII, ExoI and SbcCD nucleases are not essential for the initial targeting of RecBCD to DSBs. It is possible that the DNA-blunting activity provided by ExoVII, ExoI and SbcCD is required for an exchange of RecBCD molecules on dsDNA ends during ongoing "reckless" DNA degradation.

  2. Comparison of three methods of DNA extraction from human bones with different degrees of degradation. (United States)

    Jakubowska, Joanna; Maciejewska, Agnieszka; Pawłowski, Ryszard


    There is a necessity for deceased identification as a result of many accidents and sometimes bones are the only accessible source of DNA. So far, a universal method that allows for extraction of DNA from materials at different stages of degradation does not exist. The aims of this study were: the comparison of three methods of DNA extraction from bones with different degree of degradation and an evaluation of the usefulness of these methods in forensic genetics. The efficiency of DNA extraction, the degree of extract contamination by polymerase chain reaction (PCR) inhibitors and the possibility of determining the STR loci profile were especially being compared. Nuclear DNA from bones at different states of degradation was isolated using three methods: classical, organic phenol-chloroform extraction, DNA extraction from crystal aggregates and extraction by total demineralisation. Total demineralisation is the best method for most cases of DNA extraction from bones, although it does not provide pure DNA. DNA extraction from aggregates removes inhibitors much better and is also a good method of choice when identity determination of exhumed remains is necessary. In the case of not buried bones (remains found outside) total demineralisation or phenol-chloroform protocols are more efficient for successful DNA extraction.

  3. Barley aleurone cell death is not apoptotic: characterization of nuclease activities and DNA degradation. (United States)

    Fath, A; Bethke, P C; Jones, R L


    Barley aleurone cells undergo programmed cell death (PCD) when exposed to gibberellic acid (GA), but incubation in abscisic acid (ABA) prevent PCD. We tested the hypothesis that PCD in aleurone cells occurs by apoptosis, and show that the hallmark of apoptosis, namely DNA cleavage into 180 bp fragments, plasma membrane blebbing, and the formation of apoptotic bodies do not occur when aleurone cells die. We show that endogenous barley aleurone nucleases and nucleases present in enzymes used for protoplast preparation degrade aleurone DNA and that DNA degradation by these nucleases is rapid and can result in the formation of 180 bp DNA ladders. Methods are described that prevent DNA degradation during isolation from aleurone layers or protoplasts. Barley aleurone cells contain three nucleases whose activities are regulated by GA and ABA. CA induction and ABA repression of nuclease activities correlate with PCD in aleurone cells. Cells incubated in ABA remain alive and do not degrade their DNA, but living aleurone cells treated with GA accumulate nucleases and hydrolyze their nuclear DNA. We propose that barley nucleases play a role in DNA cleavage during aleurone PCD.

  4. Integrative bacterial artificial chromosomes for DNA integration into the Bacillus subtilis chromosome. (United States)

    Juhas, Mario; Ajioka, James W


    Bacillus subtilis is a well-characterized model bacterium frequently used for a number of biotechnology and synthetic biology applications. Novel strategies combining the advantages of B. subtilis with the DNA assembly and editing tools of Escherichia coli are crucial for B. subtilis engineering efforts. We combined Gibson Assembly and λ red recombineering in E. coli with RecA-mediated homologous recombination in B. subtilis for bacterial artificial chromosome-mediated DNA integration into the well-characterized amyE target locus of the B. subtilis chromosome. The engineered integrative bacterial artificial chromosome iBAC(cav) can accept any DNA fragment for integration into B. subtilis chromosome and allows rapid selection of transformants by B. subtilis-specific antibiotic resistance and the yellow fluorescent protein (mVenus) expression. We used the developed iBAC(cav)-mediated system to integrate 10kb DNA fragment from E. coli K12 MG1655 into B. subtilis chromosome. iBAC(cav)-mediated chromosomal integration approach will facilitate rational design of synthetic biology applications in B. subtilis.

  5. Serum induced degradation of 3D DNA box origami observed by high speed atomic force microscope

    DEFF Research Database (Denmark)

    Jiang, Zaixing; Zhang, Shuai; Yang, Chuanxu;


    3D DNA origami holds tremendous potential to encapsulate and selectively release therapeutic drugs. Observations of real-time performance of 3D DNA origami structures in physiological environment will contribute much to its further applications. Here, we investigate the degradation kinetics of 3D...... DNA box origami in serum using high-speed atomic force microscope optimized for imaging 3D DNA origami in real time. The time resolution allows characterizing the stages of serum effects on individual 3D DNA box origami with nanometer resolution. Our results indicate that the whole digest process...... is a combination of a rapid collapse phase and a slow degradation phase. The damages of box origami mainly happen in the collapse phase. Thus, the structure stability of 3D DNA box origami should be further improved, especially in the collapse phase, before clinical applications...


    Directory of Open Access Journals (Sweden)

    Andrei Stefan


    Full Text Available The aim of this study is to follow the changes that occur, in time, at DNA level and to establish an efficient and reliable protocol for ancestral DNA extraction from bones found in archaeological sites. To test whether the protocol is efficient and capable of yielding good quality DNA, extraction was first performed on fresh bones. The material consists of fresh pig (Sus scrofa and cow (Bos taurus bones that were grounded by using a drill operating at low speed. The bone powder was then incubated in lysis buffer in the presence of proteinase K. DNA isolation and purification were done by using the phenol:chloroform protocol and DNA was precipitated with absolute ethanol stored at -20oC. The extractions were carried out once every month for a total of four extractions

  7. Singlet oxygen mediated DNA degradation by copper nanoparticles: potential towards cytotoxic effect on cancer cells (United States)


    The DNA degradation potential and anti-cancer activities of copper nanoparticles of 4-5 nm size are reported. A dose dependent degradation of isolated DNA molecules by copper nanoparticles through generation of singlet oxygen was observed. Singlet oxygen scavengers such as sodium azide and Tris [hydroxyl methyl] amino methane were able to prevent the DNA degradation action of copper nanoparticles confirming the involvement of activated oxygen species in the degradation process. Additionally, it was observed that the copper nanoparticles are able to exert cytotoxic effect towards U937 and Hela cells of human histiocytic lymphoma and human cervical cancer origins, respectively by inducing apoptosis. The growth characteristics of U937 and Hela cells were studied applying various concentrations of the copper nanoparticles. PMID:21439072

  8. Singlet oxygen mediated DNA degradation by copper nanoparticles: potential towards cytotoxic effect on cancer cells

    Directory of Open Access Journals (Sweden)

    Sengupta Tapas K


    Full Text Available Abstract The DNA degradation potential and anti-cancer activities of copper nanoparticles of 4-5 nm size are reported. A dose dependent degradation of isolated DNA molecules by copper nanoparticles through generation of singlet oxygen was observed. Singlet oxygen scavengers such as sodium azide and Tris [hydroxyl methyl] amino methane were able to prevent the DNA degradation action of copper nanoparticles confirming the involvement of activated oxygen species in the degradation process. Additionally, it was observed that the copper nanoparticles are able to exert cytotoxic effect towards U937 and Hela cells of human histiocytic lymphoma and human cervical cancer origins, respectively by inducing apoptosis. The growth characteristics of U937 and Hela cells were studied applying various concentrations of the copper nanoparticles.

  9. Effect of inhibitors of cellular metabolism on postradiation repair and degradation of DNA in rat thymocytes

    Energy Technology Data Exchange (ETDEWEB)

    Ivannik, B.P.; Golubeva, R.V.; Proskuryakov, S.Ya.; Murzaev, V.I.; Ryabchenko, N.I.


    The viscosimetric method was used to determine the molecular weight of high polymer single-stranded DNA in alkaline nuclear lysates for the study of the effects of a number of inhibitors of synthesis of DNA (hydroxyurea), macroergic elements (2,4-dinitrophenol, EDTA) and DNAase (Na/sup +/ citrate, Ca/sup + +/ ions) on the process of repair and secondary post-radiation degradation of DNA of rat thymocytes exposed to radiation in a dosage of 3 kR.

  10. Action of hydrogen peroxide on degradation of DNA after irradiation in Escherichia coli. (United States)

    Keller, K M; Pollard, E C


    Hydrogen peroxide (H2O2), which produces breaks in cellular DNA, has not hitherto been shown to cause degradation of DNA. In this investigation it is shown that if transcription is blocked with rifampin, treatment with H2O2 causes degradation of DNA to nearly the same extent as does gamma-radiation. Further, if cells are given a treatment with H2O2 and incubated for 50 min, the amount of degradation in a second treatment is markedly less. This is attributed to the induction of the inhibitor of post-irradiation degradation of DNA (prd) by the first treatment. There is thus a double action of H2O2: first, to induce inhibition, and second, to cause degradation of DNA to begin in non-induced cells. The genetic dependence of induction by H2O2 mimics that of ionizing radiation. Accordingly, the induction process does not occur in recA- and lex- cells, because they are not inducible and is absent in recB- cells because they lack exonuclease V, the major component of prd. Potassium iodide (KI), an OH radical scavenger, negates the action of peroxide on DNA. The results obtained in this study suggest a possible theory for the evolution of radiation response systems

  11. Degradation of transgene DNA in genetically modified herbicide-tolerant rice during food processing. (United States)

    Song, Shangxin; Zhou, Guanghong; Gao, Feng; Zhang, Wei; Qiu, Liangyan; Dai, Sifa; Xu, Xinglian; Xiao, Hongmei


    In order to assess the effect of food processing on the degradation of exogenous DNA components in sweet rice wine and rice crackers made from genetically modified (GM) rice (Oryza sativa L.), we developed genomic DNA extraction methods and compared the effect of different food processing procedures on DNA degradation. It was found that the purity, quantity and quality of DNA by alkaline lysis method were higher than by CTAB (cetyltrimethylammonium bromide) method. For sweet rice wine, CAMV35S (cauliflower mosaic virus 35S) promoter and NOS (nopaline synthase) terminator were degraded by the third day, whereas the exogenous gene Bar (bialaphos resistance) remained unaffected. For rice crackers, boiling, drying and microwaving contributed to the initial degradations of DNA. Baking resulted in further degradations, and frying led to the most severe changes. These results indicated that the stability of DNA in GM rice was different under different processing conditions. For sweet rice wine, Bar was most stable, followed by NOS, CAMV35S, and SPS. For rice crackers, CAMV35S was most stable, followed by SPS, NOS, and Bar.

  12. Generation of an artificial skin construct containing a non-degradable fiber mesh: a potential transcutaneous interface

    Energy Technology Data Exchange (ETDEWEB)

    Cahn, Frederick [Biomedical Strategies Inc., San Diego, CA (United States); Kyriakides, Themis R [Vascular Biology and Therapeutics, Yale University, New Haven, CT 06536-9812 (United States)], E-mail:


    Generation of a stable interface between soft tissues and biomaterials could improve the function of transcutaneous prostheses, primarily by minimizing chronic infections. We hypothesized that inclusion of non-biodegradable biomaterials in an artificial skin substrate would improve integration of the neodermis. In the present study, we compared the biocompatibility of an experimental substrate, consisting of collagen and glycosylaminoglycans, with commercially available artificial skin of similar composition. By utilizing a mouse excisional wound model, we found that the source of collagen (bovine tendon versus hide), extent of injury and wound contraction were critical determinants of inflammation and neodermis formation. Reducing the extent of injury to underlying muscle reduced inflammation and improved remodeling; the improved conditions allowed the detection of a pro-inflammatory effect of hide-derived collagen. To eliminate the complication of wound contraction, subsequent grafts were performed in guinea pigs and showed that inclusion of carbon fibers or non-degradable sutures resulted in increased foreign body response (FBR) and altered remodeling. On the other hand, inclusion of a polyester multi-stranded mesh induced a mild FBR and allowed normal neodermis formation. Taken together, our observations suggest that non-degradable biomaterials can be embedded in an artificial skin construct without compromising its ability to induce neodermis formation.

  13. Maternal inheritance of mitochondrial DNA: degradation of paternal mitochondria by allogeneic organelle autophagy, allophagy. (United States)

    Sato, Miyuki; Sato, Ken


    Maternal inheritance of mitochondrial DNA (mtDNA) is generally observed in many eukaryotes. Sperm-derived paternal mitochondria and their mtDNA enter the oocyte cytoplasm upon fertilization and then normally disappear during early embryogenesis. However, the mechanism underlying this clearance of paternal mitochondria has remained largely unknown. Recently, we showed that autophagy is required for the elimination of paternal mitochondria in Caenorhabditis elegans embryos. Shortly after fertilization, autophagosomes are induced locally around the penetrated sperm components. These autophagosomes engulf paternal mitochondria, resulting in their lysosomal degradation during early embryogenesis. In autophagy-defective zygotes, paternal mitochondria and their genomes remain even in the larval stage. Therefore, maternal inheritance of mtDNA is accomplished by autophagic degradation of paternal mitochondria. We also found that another kind of sperm-derived structure, called the membranous organelle, is degraded by zygotic autophagy as well. We thus propose to term this allogeneic (nonself) organelle autophagy as allophagy.

  14. Cut-and-Paste of DNA Using an Artificial Restriction DNA Cutter

    Directory of Open Access Journals (Sweden)

    Makoto Komiyama


    Full Text Available DNA manipulations using a completely chemistry-based DNA cutter (ARCUT have been reviewed. This cutter, recently developed by the authors, is composed of Ce(IV/EDTA complex and two strands of pseudo-complementary peptide nucleic acid. The site-selective scission proceeds via hydrolysis of targeted phosphodiester linkages, so that the resultant scission fragments can be easily ligated with other fragments by using DNA ligase. Importantly, scission-site and site-specificity of the cutter are freely tuned in terms of the Watson–Crick rule. Thus, when one should like to manipulate DNA according to the need, he or she does not have to think about (1 whether appropriate “restriction enzyme sites” exist near the manipulation site and (2 whether the site-specificity of the restriction enzymes, if any, are sufficient to cut only the aimed position without chopping the DNA at non-targeted sites. Even the human genome can be manipulated, since ARCUT can cut the genome at only one predetermined site. Furthermore, the cutter is useful to promote homologous recombination in human cells, converting a site to desired sequence. The ARCUT-based DNA manipulation should be promising for versatile applications.

  15. DNA-Mediated Self-Organization of Polymeric Nanocompartments Leads to Interconnected Artificial Organelles. (United States)

    Liu, Juan; Postupalenko, Viktoriia; Lörcher, Samuel; Wu, Dalin; Chami, Mohamed; Meier, Wolfgang; Palivan, Cornelia G


    Self-organization of nanocomponents was mainly focused on solid nanoparticles, quantum dots, or liposomes to generate complex architectures with specific properties, but intrinsically limited or not developed enough, to mimic sophisticated structures with biological functions in cells. Here, we present a biomimetic strategy to self-organize synthetic nanocompartments (polymersomes) into clusters with controlled properties and topology by exploiting DNA hybridization to interconnect polymersomes. Molecular and external factors affecting the self-organization served to design clusters mimicking the connection of natural organelles: fine-tune of the distance between tethered polymersomes, different topologies, no fusion of clustered polymersomes, and no aggregation. Unexpected, extended DNA bridges that result from migration of the DNA strands inside the thick polymer membrane (about 12 nm) represent a key stability and control factor, not yet exploited for other synthetic nano-object networks. The replacement of the empty polymersomes with artificial organelles, already reported for single polymersome architecture, will provide an excellent platform for the development of artificial systems mimicking natural organelles or cells and represents a fundamental step in the engineering of molecular factories.

  16. Proteasome-dependent degradation of replisome components regulates faithful DNA replication. (United States)

    Roseaulin, Laura C; Noguchi, Chiaki; Noguchi, Eishi


    The replication machinery, or the replisome, collides with a variety of obstacles during the normal process of DNA replication. In addition to damaged template DNA, numerous chromosome regions are considered to be difficult to replicate owing to the presence of DNA secondary structures and DNA-binding proteins. Under these conditions, the replication fork stalls, generating replication stress. Stalled forks are prone to collapse, posing serious threats to genomic integrity. It is generally thought that the replication checkpoint functions to stabilize the replisome and replication fork structure upon replication stress. This is important in order to allow DNA replication to resume once the problem is solved. However, our recent studies demonstrated that some replisome components undergo proteasome-dependent degradation during DNA replication in the fission yeast Schizosaccharomyces pombe. Our investigation has revealed the involvement of the SCF(Pof3) (Skp1-Cullin/Cdc53-F-box) ubiquitin ligase in replisome regulation. We also demonstrated that forced accumulation of the replisome components leads to abnormal DNA replication upon replication stress. Here we review these findings and present additional data indicating the importance of replisome degradation for DNA replication. Our studies suggest that cells activate an alternative pathway to degrade replisome components in order to preserve genomic integrity.

  17. Targeting DNA base pair mismatch with artificial nucleobases. Advances and perspectives in triple helix strategy. (United States)

    Malnuit, Vincent; Duca, Maria; Benhida, Rachid


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

  18. Phytoremediation potential of duckweed (Lemna minor L.) in degradation of C.I. Acid Blue 92: artificial neural network modeling. (United States)

    Khataee, A R; Movafeghi, A; Torbati, S; Salehi Lisar, S Y; Zarei, M


    In present study, the potential of duckweed (Lemna minor L.) for degradation of an azo dye C.I. Acid Blue 92 (AB92) has been investigated. The effect of operational parameters such as initial dye concentration, pH, temperature and amount of plant on the efficiency of biological decolorization process was determined. The reusability of Lemna minor L. in long term repetitive operations was also examined. Growth and some biochemical parameters (photosynthetic pigments content, superoxide dismutase, catalase and peroxidase activity) were used to detect the toxic effects of AB92 on duckweed plant. The biological degradation compounds formed in the present process were analyzed by GC-MS technique. In addition, an artificial neural network (ANN) model was expanded to predict the biological decolorization efficiency. The obtained data indicated that ANN provide realistic predictive performance (R(2)=0.954). Copyright © 2012 Elsevier Inc. All rights reserved.

  19. The development of miniplex primer sets for the analysis of degraded DNA (United States)

    McCord, Bruce; Opel, Kerry; Chung, Denise; Drabek, Jiri; Tatarek, Nancy; Meadows Jantz, Lee; Butler, John


    In this project, a new set of multiplexed PCR reactions has been developed for the analysis of degraded DNA. These DNA markers, known as Miniplexes, utilize primers that have shorter amplicons for use in short tandem repeat (STR) analysis of degraded DNA. In our work we have defined six of these new STR multiplexes, each of which consists of 3 to 4 reduced size STR loci, and each labeled with a different fluorescent dye. When compared to commercially available STR systems, reductions in size of up to 300 basepairs are possible. In addition, these newly designed amplicons consist of loci that are fully compatible with the the national computer DNA database known as CODIS. To demonstrate compatibility with commercial STR kits, a concordance study of 532 DNA samples of Caucasian, African American, and Hispanic origin was undertaken There was 99.77% concordance between allele calls with the two methods. Of these 532 samples, only 15 samples showed discrepancies at one of 12 loci. These occurred predominantly at 2 loci, vWA and D13S317. DNA sequencing revealed that these locations had deletions between the two primer binding sites. Uncommon deletions like these can be expected in certain samples and will not affect the utility of the Miniplexes as tools for degraded DNA analysis. The Miniplexes were also applied to enzymatically digested DNA to assess their potential in degraded DNA analysis. The results demonstrated a greatly improved efficiency in the analysis of degraded DNA when compared to commercial STR genotyping kits. A series of human skeletal remains that had been exposed to a variety of environmental conditions were also examined. Sixty-four percent of the samples generated full profiles when amplified with the Miniplexes, while only sixteen percent of the samples tested generated full profiles with a commercial kit. In addition, complete profiles were obtained for eleven of the twelve Miniplex loci which had amplicon size ranges less than 200 base pairs

  20. NUC-1, a caenorhabditis elegans DNase II homolog, functions in an intermediate step of DNA degradation during apoptosis. (United States)

    Wu, Y C; Stanfield, G M; Horvitz, H R


    One hallmark of apoptosis is the degradation of chromosomal DNA. We cloned the Caenorhabditis elegans gene nuc-1, which is involved in the degradation of the DNA of apoptotic cells, and found that nuc-1 encodes a homolog of mammalian DNase II. We used the TUNEL technique to assay DNA degradation in nuc-1 and other mutants defective in programmed cell death and discovered that TUNEL labels apoptotic cells only during a transient intermediate stage. Mutations in nuc-1 allowed the generation of TUNEL-reactive DNA but blocked the conversion of TUNEL-reactive DNA to a subsequent TUNEL-unreactive state. Completion of DNA degradation did not occur in the absence of cell-corpse engulfment. Our data suggest that the process of degradation of the DNA of a cell corpse occurs in at least three distinct steps and requires activities provided by both the dying and the engulfing cell.

  1. Self-assembled nanoscale DNA-porphyrin complex for artificial light harvesting. (United States)

    Woller, Jakob G; Hannestad, Jonas K; Albinsson, Bo


    Mimicking green plants' and bacteria's extraordinary ability to absorb a vast number of photons and harness their energy is a longstanding goal in artificial photosynthesis. Resonance energy transfer among donor dyes has been shown to play a crucial role on the overall transfer of energy in the natural systems. Here, we present artificial, self-assembled, light-harvesting complexes consisting of DNA scaffolds, intercalated YO-PRO-1 (YO) donor dyes and a porphyrin acceptor anchored to a lipid bilayer, conceptually mimicking the natural light-harvesting systems. A model system consisting of 39-mer duplex DNA in a linear wire configuration with the porphyrin attached in the middle of the wire is primarily investigated. Utilizing intercalated donor fluorophores to sensitize the excitation of the porphyrin acceptor, we obtain an effective absorption coefficient 12 times larger than for direct excitation of the porphyrin. On the basis of steady-state and time-resolved emission measurements and Markov chain simulations, we show that YO-to-YO resonance energy transfer substantially contributes to the overall flow of energy to the porphyrin. This increase is explained through energy migration along the wire allowing the excited state energy to transfer to positions closer to the porphyrin. The versatility of DNA as a structural material is demonstrated through the construction of a more complex, hexagonal, light-harvesting scaffold yielding further increase in the effective absorption coefficient. Our results show that, by using DNA as a scaffold, we are able to arrange chromophores on a nanometer scale and in this way facilitate the assembly of efficient light-harvesting systems.

  2. Kinetics of carbaryl degradation by anodic Fenton treatment in a humic-acid-amended artificial soil slurry. (United States)

    Ye, Peng; Kong, Lingjun; Lemley, Ann T


    A Fenton-based indirect electrochemical method, anodic Fenton treatment (AFT), developed for destroying and detoxifying pesticides in the aqueous environment, was evaluated for the degradation of a widely used pesticide, carbaryl, in an artificial soil slurry. More than 90% of carbaryl was removed in less than 20 minutes under given experimental conditions. The effect of initial slurry pH, humic acid content, initial carbaryl concentration, Fenton reagent delivery ratio, and soil/water ratio (w/v) were investigated. The results indicate that humic acid content is the key factor that slows down pesticide degradation, most probably because of its pH buffering and adsorption capacity. A kinetic model, which was shown to fit the experimental data quite well (R2 > 0.99), was developed to describe the carbaryl degradation in the soil slurry during the AFT process. In the presence of humic acid, carbaryl degradation kinetics was found to shift to a pseudo-first-order reaction after an "initiation" stage.

  3. Modulation of eDNA release and degradation affects Staphylococcus aureus biofilm maturation.

    Directory of Open Access Journals (Sweden)

    Ethan E Mann

    Full Text Available Recent studies have demonstrated a role for Staphylococcus aureus cidA-mediated cell lysis and genomic DNA release in biofilm adherence. The current study extends these findings by examining both temporal and additional genetic factors involved in the control of genomic DNA release and degradation during biofilm maturation. Cell lysis and DNA release were found to be critical for biofilm attachment during the initial stages of development and the released DNA (eDNA remained an important matrix component during biofilm maturation. This study also revealed that an lrgAB mutant exhibits increased biofilm adherence and matrix-associated eDNA consistent with its proposed role as an inhibitor of cidA-mediated lysis. In flow-cell assays, both cid and lrg mutations had dramatic effects on biofilm maturation and tower formation. Finally, staphylococcal thermonuclease was shown to be involved in biofilm development as a nuc mutant formed a thicker biofilm containing increased levels of matrix-associated eDNA. Together, these findings suggest a model in which the opposing activities of the cid and lrg gene products control cell lysis and genomic DNA release during biofilm development, while staphylococcal thermonuclease functions to degrade the eDNA, possibly as a means to promote biofilm dispersal.

  4. DNA degradation within mouse brain and dental pulp cells 72 hours postmortem

    Institute of Scientific and Technical Information of China (English)

    Jilong Zheng; Xiaona Li; Di Shan; Han Zhang; Dawei Guan


    In this study, we sought to elucidate the process of DNA degradation in brain and dental pulp cells of mice, within postmortem 0-72 hours, by using the single cell gel electrophoresis assay and professional comet image analysis and processing techniques. The frequency of comet-like cells, the percentage of tail DNA, tail length, tail moment, Olive moment and tail area increased in tandem with increasing postmortem interval. In contrast, the head radius, the percentage of head DNA and head area showed a decreasing trend. Linear regression analysis revealed a high correlation between these parameters and the postmortem interval. The findings suggest that the single cell gel electrophoresis assay is a quick and sensitive method to detect DNA degradation in brain and dental pulp cells, providing an objective and accurate new way to estimate postmortem interval.

  5. An enzyme-based DNA preparation method for application to forensic biological samples and degraded stains. (United States)

    Lounsbury, Jenny A; Coult, Natalie; Miranian, Daniel C; Cronk, Stephen M; Haverstick, Doris M; Kinnon, Paul; Saul, David J; Landers, James P


    Extraction of DNA from forensic samples typically uses either an organic extraction protocol or solid phase extraction (SPE) and these methods generally involve numerous sample transfer, wash and centrifugation steps. Although SPE has been successfully adapted to the microdevice, it can be problematic because of lengthy load times and uneven packing of the solid phase. A closed-tube enzyme-based DNA preparation method has recently been developed which uses a neutral proteinase to lyse cells and degrade proteins and nucleases [14]. Following a 20 min incubation of the buccal or whole blood sample with this proteinase, DNA is polymerase chain reaction (PCR)-ready. This paper describes the optimization and quantitation of DNA yield using this method, and application to forensic biological samples, including UV- and heat-degraded whole blood samples on cotton or blue denim substrates. Results demonstrate that DNA yield can be increased from 1.42 (±0.21)ng/μL to 7.78 (±1.40)ng/μL by increasing the quantity of enzyme per reaction by 3-fold. Additionally, there is a linear relationship between the amount of starting cellular material added and the concentration of DNA in the solution, thereby allowing DNA yield estimations to be made. In addition, short tandem repeat (STR) profile results obtained using DNA prepared with the enzyme method were comparable to those obtained with a conventional SPE method, resulting in full STR profiles (16 of 16 loci) from liquid samples (buccal swab eluate and whole blood), dried buccal swabs and bloodstains and partial profiles from UV or heat-degraded bloodstains on cotton or blue denim substrates. Finally, the DNA preparation method is shown to be adaptable to glass or poly(methyl methacrylate) (PMMA) microdevices with little impact on STR peak height but providing a 20-fold reduction in incubation time (as little as 60 s), leading to a ≥1 h reduction in DNA preparation time.

  6. Model-based analysis of photoinitiated coating degradation under artificial exposure conditions

    DEFF Research Database (Denmark)

    Kiil, Søren


    Coating degradation mechanisms of thermoset coatings exposed to ultraviolet radiation and humidity at constant temperature are investigated. The essential processes, photoinitiated oxidation reactions, intrafilm oxygen permeability, water absorption and diffusion, reduction of crosslink density...

  7. The roles and acting mechanism of Caenorhabditis elegans DNase II genes in apoptotic dna degradation and development.

    Directory of Open Access Journals (Sweden)

    Huey-Jen Lai

    Full Text Available DNase II enzymes are acidic endonucleases that have been implicated in mediating apoptotic DNA degradation, a critical cell death execution event. C. elegans genome contains three DNase II homologues, NUC-1, CRN-6, and CRN-7, but their expression patterns, acting sites, and roles in apoptotic DNA degradation and development are unclear. We have conducted a comprehensive analysis of three C. elegans DNase II genes and found that nuc-1 plays a major role, crn-6 plays an auxiliary role, and crn-7 plays a negligible role in resolving 3' OH DNA breaks generated in apoptotic cells. Promoter swapping experiments suggest that crn-6 but not crn-7 can partially substitute for nuc-1 in mediating apoptotic DNA degradation and both fail to replace nuc-1 in degrading bacterial DNA in intestine. Despite of their restricted and largely non-overlapping expression patterns, both CRN-6 and NUC-1 can mediate apoptotic DNA degradation in many cells, suggesting that they are likely secreted nucleases that are retaken up by other cells to exert DNA degradation functions. Removal or disruption of NUC-1 secretion signal eliminates NUC-1's ability to mediate DNA degradation across its expression border. Furthermore, blocking cell corpse engulfment does not affect apoptotic DNA degradation mediated by nuc-1, suggesting that NUC-1 acts in apoptotic cells rather than in phagocytes to resolve 3' OH DNA breaks. Our study illustrates how multiple DNase II nucleases play differential roles in apoptotic DNA degradation and development and reveals an unexpected mode of DNase II action in mediating DNA degradation.

  8. Degradation of benzotriazole and benzothiazole in treatment wetlands and by artificial sunlight. (United States)

    Felis, Ewa; Sochacki, Adam; Magiera, Sylwia


    Laboratory-scale experiments were performed using unsaturated subsurface-flow treatment wetlands and artificial sunlight (with and without TiO2) to study the efficiency of benzotriazole and benzothiazole removal and possible integration of these treatment methods. Transformation products in the effluent from the treatment wetlands and the artificial sunlight reactor were identified by high performance liquid chromatography coupled with tandem mass spectrometry. The removal of benzothiazole in the vegetated treatment wetlands was 99.7%, whereas the removal of benzotriazole was 82.8%. The vegetation positively affected only the removal of benzothiazole. The major transformation products in the effluents from the treatment wetlands were methylated and hydroxylated derivatives of benzotriazole, and hydroxylated derivatives of benzothiazole. Hydroxylation was found to be the main process governing the transformation pathway for both compounds in the artificial sunlight experiment (with and without TiO2). Benzotriazole was not found to be susceptible to photodegradation in the absence of TiO2. The integration of the sunlight-induced processes (with TiO2) with subsurface-flow treatment wetlands caused further elimination of the compounds (42% for benzotriazole and 58% for benzothiazole). This was especially significant for the elimination of benzotriazole, because the removal of this compound was 96% in the coupled processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Determination of the Early Time of Death by Computerized Image Analysis of DNA Degradation: Which Is the Best Quantitative Indicator of DNA Degradation?

    Institute of Scientific and Technical Information of China (English)

    LIU Lijiang; SHU Xiji; REN Liang; ZHOU Hongyan; LI Yan; LIU Wei; ZHU Cheng; LIU Liang


    This study evaluated the correlation between DNA degradation of the splenic lymphocytes and the early time of death, examined the early time of death by computerized image analysis technique (CIAT) and identified the best parameter that quantitatively reflects the DNA degradation.The spleen tissues from 34 SD rats were collected, subjected to cell smearing every 2 h within the first 36 h after death, stained by Feulgen-Van's staining, three indices reflecting DNA content in splenic lymphocytes, including integral optical density (IOD), average optical density (AOD), average gray scale (AG) were measured by the image analysis. Our results showed that IOD and AOD decreased and AG increased over time within the first 36 h. A stepwise linear regression analysis showed that only AG was fitted. A correlation between the postmortem interval (PMI) and AG was identified and the corresponding regression equation was obtained. Our study suggests that CIAT is a useful and promising tool for the estimation of early PMI with good objectivity and reproducibility,and AG is a more effective and better quantitative indicator for the estimation of PMI within the first 36 h after death in rats.

  10. Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

    Directory of Open Access Journals (Sweden)

    Emma Werz


    Full Text Available The article describes the immobilization of different probe oligonucleotides (4, 7, 10 carrying each a racemic mixture of 2,3-bis(hexadecyloxypropan-1-ol (1a at the 5’-terminus on a stable artificial lipid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC. The bilayer separates two compartments (cis/trans channel of an optical transparent microfluidic sample carrier with perfusion capabilities. Injection of unlabeled target DNA sequences (6, 8, or 9, differing in sequence and length, leads in the case of complementarity to the formation of stable DNA duplexes at the bilayer surface. This could be verified by Sybr Green I double strand staining, followed by incubation periods and thorough perfusions, and was visualized by single molecule fluorescence spectroscopy and microscopy. The different bilayer-immobilized complexes consisting of various DNA duplexes and the fluorescent dye were studied with respect to the kinetics of their formation as well as to their stability against perfusion.

  11. Evaluating portland cement concrete degradation by sulphate exposure through artificial neural networks modeling

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Douglas Nunes de; Bourguignon, Lucas Gabriel Garcia; Tolentino, Evandro, E-mail: [Centro Federal de Educacao Tecnologica de Minas Gerais (CEFET-MG), Timoteo, MG (Brazil); Costa, Rodrigo Moyses, E-mail: [Universidade de Itauna, Itauna, MG (Brazil); Tello, Cledola Cassia Oliveira de, E-mail: [Centro de Desenvolvimento da Tecnologia Nucelar (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)


    A concrete is durable if it has accomplished the desired service life in the environment in which it is exposed. The durability of concrete materials can be limited as a result of adverse performance of its cement-paste matrix or aggregate constituents under either chemical or physical attack. Among other aggressive chemical exposures, the sulphate attack is an important concern. Water, soils and gases, which contain sulphate, represent a potential threat to the durability of concrete structures. Sulphate attack in concrete leads to the conversion of the hydration products of cement to ettringite, gypsum, and other phases, and also it leads to the destabilization of the primary strength generating calcium silicate hydrate (C-S-H) gel. The formation of ettringite and gypsum is common in cementitious systems exposed to most types of sulphate solutions. The present work presents the application of the neural networks for estimating deterioration of various concrete mixtures due to exposure to sulphate solutions. A neural networks model was constructed, trained and tested using the available database. In general, artificial neural networks could be successfully used in function approximation problems in order to approach the data generation function. Once data generation function is known, artificial neural network structure is tested using data not presented to the network during training. This paper is intent to provide the technical requirements related to the production of a durable concrete to be used in the structures of the Brazilian near-surface repository of radioactive wastes. (author)

  12. Degradation of the cancer genomic DNA deaminase APOBEC3B by SIV Vif. (United States)

    Land, Allison M; Wang, Jiayi; Law, Emily K; Aberle, Ryan; Kirmaier, Andrea; Krupp, Annabel; Johnson, Welkin E; Harris, Reuben S


    APOBEC3B is a newly identified source of mutation in many cancers, including breast, head/neck, lung, bladder, cervical, and ovarian. APOBEC3B is a member of the APOBEC3 family of enzymes that deaminate DNA cytosine to produce the pro-mutagenic lesion, uracil. Several APOBEC3 family members function to restrict virus replication. For instance, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H combine to restrict HIV-1 in human lymphocytes. HIV-1 counteracts these APOBEC3s with the viral protein Vif, which targets the relevant APOBEC3s for proteasomal degradation. While APOBEC3B does not restrict HIV-1 and is not targeted by HIV-1 Vif in CD4-positive T cells, we asked whether related lentiviral Vif proteins could degrade APOBEC3B. Interestingly, several SIV Vif proteins are capable of promoting APOBEC3B degradation, with SIVmac239 Vif proving the most potent. This likely occurs through the canonical polyubiquitination mechanism as APOBEC3B protein levels are restored by MG132 treatment and by altering a conserved E3 ligase-binding motif. We further show that SIVmac239 Vif can prevent APOBEC3B mediated geno/cytotoxicity and degrade endogenous APOBEC3B in several cancer cell lines. Our data indicate that the APOBEC3B degradation potential of SIV Vif is an effective tool for neutralizing the cancer genomic DNA deaminase APOBEC3B. Further optimization of this natural APOBEC3 antagonist may benefit cancer therapy.

  13. The development of reduced size STR amplicons as tools for analysis of degraded DNA. (United States)

    Butler, John M; Shen, Yin; McCord, Bruce R


    New multiplex PCR sets of commonly used short tandem repeat (STR) markers have been developed to produce PCR products that are reduced in size when compared to standard commercial STR kits. The reduction in size of these amplicons can facilitate the examination and analysis of degraded DNA evidence by improving amplification efficiency. This "miniSTR" approach will permit current forensic practitioners to use STR markers and instrumentation already present in their laboratories and to generate genotyping data that is directly comparable to reference samples and searchable through the FBI's Combined DNA Index System (CODIS) databases. This paper discusses the development of these new primer sets and presents some initial results in the analysis of degraded and aged DNA samples. A method for removal of problematic fluorescent dye artifacts is also described. Comparison studies in over 100 samples have verified that these miniSTR primers can provide fully concordant results to commercial STR kits and can provide improved signal from degraded DNA specimens. These miniplex sets should prove valuable in the analysis of samples where allele dropout and reduced sensitivity of larger STR alleles occurs.

  14. Dual-degradable disulfide-containing PEI–Pluronic/DNA polyplexes: transfection efficiency and balancing protection and DNA release

    Directory of Open Access Journals (Sweden)

    Zhang L


    Full Text Available Lifen Zhang,* Zhenzhen Chen,* Yanfeng LiState Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Institute of Biochemical Engineering and Environmental Technology, Lanzhou University, Lanzhou, People's Republic of China*These authors contributed equally to this workAbstract: Polymeric gene-delivery vectors to achieve lack of toxicity and a balance between protection and DNA release remains a formidable challenge. Incorporating intracellular environment-responsive degradable bonds is an appreciable step toward developing safer transfection agents. In this study, novel, dual-degradable polycation copolymers (Pluronic-diacrylate [PA]–polyethyleneimine [PEI]–SS were synthesized through the addition of low molecular weight (800 Da PEI cross-linked with SS (PEI-SS to PA. Three PA-PEI-SS copolymers (PA-PEI-SS1, 2, and 3 with different PEI-SS to Pluronic molar ratios were investigated and found to strongly condense plasmid DNA into positively charged nanoparticles with an average particle size of approximately 200 nm and to possess higher stability against DNase I digestion and sodium heparin. Disulfide and ester bonds of the copolymers were susceptible to intracellular redox conditions. In vitro experiments demonstrated that the PA-PEI-SS copolymers had significantly lower cytotoxicity and higher transfection efficiency in both BGC-823 and 293T cell lines than the controls of degradable PEI-SS and nondegradable 25 kDa PEI. Transfection activity was influenced by the PEI-SS content in the polymers and PA-PEI-SS1 showed the highest efficiency of the three copolymers. These studies suggest that these dual-degradable copolymers could be used as potential biocompatible gene delivery carriers.Keywords: Pluronic, PEI, gene vector, dual-degradable, disulfide-containing linker

  15. Heat degradation of eukaryotic and bacterial DNA: an experimental model for paleomicrobiology

    Directory of Open Access Journals (Sweden)

    Nguyen-Hieu Tung


    Full Text Available Abstract Background Theoretical models suggest that DNA degradation would sharply limit the PCR-based detection of both eukaryotic and prokaryotic DNA within ancient specimens. However, the relative extent of decay of eukaryote and prokaryote DNA over time is a matter of debate. In this study, the murine macrophage cell line J774, alone or infected with Mycobacterium smegmatis bacteria, were killed after exposure to 90°C dry heat for intervals ranging from 1 to 48 h in order to compare eukaryotic cells, extracellular bacteria and intracellular bacteria. The sizes of the resulting mycobacterial rpoB and murine rpb2 homologous gene fragments were then determined by real-time PCR and fluorescent probing. Findings The cycle threshold (Ct values of PCR-amplified DNA fragments from J774 cells and the M. smegmatis negative controls (without heat exposure varied from 26–33 for the J774 rpb2 gene fragments and from 24–29 for M. smegmatis rpoB fragments. After 90°C dry heat incubation for up to 48 h, the Ct values of test samples increased relative to those of the controls for each amplicon size. For each dry heat exposure time, the Ct values of the 146-149-bp fragments were lower than those of 746-747-bp fragments. During the 4- to 24-h dry heat incubation, the non-infected J774 cell DNA was degraded into 597-bp rpb2 fragments. After 48 h, however, only 450-bp rpb2 fragments of both non-infected and infected J774 cells could be amplified. In contrast, the 746-bp rpoB fragments of M. smegmatis DNA could be amplified after the 48-h dry heat exposure in all experiments. Infected and non-infected J774 cell DNA was degraded more rapidly than M. smegmatis DNA after dry heat exposure (ANOVA test, p  Conclusion In this study, mycobacterial DNA was more resistant to dry-heat stress than eukaryotic DNA. Therefore, the detection of large, experimental, ancient mycobacterial DNA fragments is a suitable approach for paleomicrobiological studies.

  16. Magnetic Scanometric DNA Microarray Detection of Methyl Tertiary Butyl Ether Degrading Bacteria for Environmental Monitoring (United States)

    Chan, Mei-Lin; Jaramillo, Gerardo; Hristova, Krassimira R.; Horsley, David A.


    A magnetoresistive biosensing platform based on a single magnetic tunnel junction (MTJ) scanning probe and DNA microarrays labeled with magnetic particles has been developed to provide an inexpensive, sensitive and reliable detection of DNA. The biosensing platform was demonstrated on a DNA microarray assay for quantifying bacteria capable of degrading methyl tertiary-butyl ether (MTBE), where concentrations as low as 10 pM were detectable. Synthetic probe bacterial DNA was immobilized on a microarray glass slide surface, hybridized with the 48 base pair long biotinylated target DNA and subsequently incubated with streptavidin-coated 2.8 μm diameter magnetic particles. The biosensing platform then makes use of a micron-sized MTJ sensor that was raster scanned across a 3 mm by 5 mm glass slide area to capture the stray magnetic field from the tagged DNA and extract two dimensional magnetic field images of the microarray. The magnetic field output is then averaged over each 100 μm diameter DNA array spot to extract the magnetic spot intensity, analogous to the fluorescence spot intensity used in conventional optical scanners. The magnetic scanning result is compared with results from a commercial laser scanner and particle coverage optical counting to demonstrate the dynamic range and linear sensitivity of the biosensing platform as a potentially inexpensive, sensitive and portable alternative for DNA microarray detection for field applications. PMID:20889328

  17. Enhanced cleavage of double-stranded DNA by artificial zinc-finger nuclease sandwiched between two zinc-finger proteins. (United States)

    Mineta, Yusuke; Okamoto, Tomoyuki; Takenaka, Kosuke; Doi, Norio; Aoyama, Yasuhiro; Sera, Takashi


    To enhance DNA cleavage by zinc-finger nucleases (ZFNs), we sandwiched a DNA cleavage enzyme with two artificial zinc-finger proteins (AZPs). Because the DNA between the two AZP-binding sites is cleaved, the AZP-sandwiched nuclease is expected to bind preferentially to a DNA substrate rather than to cleavage products and thereby cleave it with multiple turnovers. To demonstrate the concept, we sandwiched a staphylococcal nuclease (SNase), which cleaves DNA as a monomer, between two three-finger AZPs. The AZP-sandwiched SNase cleaved large amounts of dsDNA site-specifically. Such multiple-turnover cleavage was not observed with nucleases that possess a single AZP. Thus, AZP-sandwiched nucleases will further refine ZFN technology.

  18. Bifunctional composite from spent "Cyprus coffee" for tetracycline removal and phenol degradation: Solar-Fenton process and artificial neural network. (United States)

    Oladipo, Akeem Adeyemi; Abureesh, Mosab Ali; Gazi, Mustafa


    Removals of tetracycline and photocatalytic degradation of phenol by Fe3O4/coffee residue (MCC) were investigated. Brunauer-Emmett-Teller (BET), vibrating sample magnetometer (VSM) and Boehm titration were employed to characterize MCC. Artificial neural network (ANN) model was developed to predict the tetracycline (TC) concentration in the column effluent. Maximum tetracycline adsorption capacity of 285.6mg/g was observed in a batch system. High removal efficiency (87%) was obtained at 3.3mL/min flow rate, 8.0cm bed height and 50mg/L influent TC concentration in a column system. Complete degradation of phenol by solar-Fenton was attained at 60min irradiation time. Total organic carbon (TOC) removal increased to 63.3% in the presence of 1.0g/L MCC, 1.2g/L H2O2 and solar irradiation. MCC showed remarkable potential to remove antibiotics from wastewater even in the presence of heavy metal (Ni(2+)) via magnetic separation.

  19. Capillary electrophoresis of miniSTR markers to genotype highly degraded DNA samples. (United States)

    Coble, Michael D


    The amplification of short tandem repeat (STR) markers throughout the human nuclear DNA genome are used to associate crime scene evidence to the perpetrator's profile in criminal investigations. For highly challenged or compromised materials such as stains exposed to the elements, skeletal remains from missing persons cases, or fragmented and degraded samples from mass disasters, obtaining a full STR profile may be difficult if not impossible. With the introduction of short amplicon STR or "miniSTR" typing, it is possible to obtain STR genetic information from highly challenged samples without the need to sequence the hypervariable regions of the mitochondrial DNA (mtDNA) genome. Non-Combined DNA Index System (CODIS) STR markers have been developed to obtain information beyond the core CODIS loci. This chapter will focus on the steps necessary to prepare and use one of the non-CODIS (NC) multiplexes, NC01 (Coble and Butler 2005), for analysis on capillary electrophoresis instrumentation.

  20. DNA genetic artificial fish swarm constant modulus blind equalization algorithm and its application in medical image processing. (United States)

    Guo, Y C; Wang, H; Zhang, B L


    This study proposes use of the DNA genetic artificial fish swarm constant modulus blind equalization algorithm (DNA-G-AFS-CMBEA) to overcome the local convergence of the CMBEA. In this proposed algorithm, after the fusion of the fast convergence of the AFS algorithm and the global search capability of the DNA-G algorithm to drastically optimize the position vector of the artificial fish, the global optimal position vector is obtained and used as the initial optimal weight vector of the CMBEA. The result of application of this improved method in medical image processing demonstrates that the proposed algorithm outperforms the CMBEA and the AFS-CMBEA in removing the noise in a medical image and improving the peak signal to noise ratio.

  1. DDB2 association with PCNA is required for its degradation after UV-induced DNA damage. (United States)

    Cazzalini, Ornella; Perucca, Paola; Mocchi, Roberto; Sommatis, Sabrina; Prosperi, Ennio; Stivala, Lucia Anna


    DDB2 is a protein playing an essential role in the lesion recognition step of the global genome sub-pathway of nucleotide excision repair (GG-NER) process. Among the proteins involved in the DNA damage response, p21(CDKN1A) (p21) has been reported to participate in NER, but also to be removed by proteolytic degradation, thanks to its association with PCNA. DDB2 is involved in the CUL4-DDB1 complex mediating p21 degradation; however, the direct interaction between DDB2, p21 and PCNA has been never investigated. Here, we show that DDB2 co-localizes with PCNA and p21 at local UV-induced DNA-damage sites, and these proteins co-immunoprecipitate in the same complex. In addition, we provide evidence that p21 is not able to bind directly DDB2, but, to this end, the presence of PCNA is required. Direct physical association of recombinant DDB2 protein with PCNA is mediated by a conserved PIP-box present in the N-terminal region of DDB2. Mutation of the PIP-box resulted in the loss of protein interaction. Interestingly, the same mutation, or depletion of PCNA by RNA interference, greatly impaired DDB2 degradation induced by UV irradiation. These results indicate that DDB2 is a PCNA-binding protein, and that this association is required for DDB2 proteolytic degradation.

  2. Quantitative assessment of the effect of uracil-DNA glycosylase on amplicon DNA degradation and RNA amplification in reverse transcription-PCR

    Directory of Open Access Journals (Sweden)

    Kleiboeker Steven B


    Full Text Available Abstract Although PCR and RT-PCR provided a valuable approach for detection of pathogens, the high level of sensitivity of these assays also makes them prone to false positive results. In addition to cross-contamination with true positive samples, false positive results are also possible due to "carry-over" contamination of samples with amplicon DNA generated by previous reactions. To reduce this source of false positives, amplicon generated by reactions in which dUTP was substituted for dTTP can be degraded by uracil DNA glycosylase (UNG. UNG does not degrade RNA but will cleave contaminating uracil-containing DNA while leaving thymine-containing DNA intact. The availability of heat-labile UNG makes use of this approach feasible for RT-PCR. In this study, real-time RT-PCR was used to quantify UNG degradation of amplicon DNA and the effect of UNG on RNA detection. Using the manufacturers' recommended conditions, complete degradation of DNA was not observed for samples containing 250 copies of amplicon DNA. Doubling the UNG concentration resulted in degradation of the two lowest concentrations of DNA tested, but also resulted in an increase of 1.94 cycles in the CT for RNA detection. To improve DNA degradation while minimizing the effect on RNA detection, a series of time, temperature and enzyme concentrations were evaluated. Optimal conditions were found to be 0.25 U UNG per 25 μl reaction with a 20 min, 30°C incubation prior to RT-PCR. Under these conditions, high concentrations of amplicon DNA could be degraded while the CT for RNA detection was increased by 1.2 cycles.

  3. Acceleration of Long-Range Photoinduced Electron Transfer through DNA by Hydroxyquinolines as Artificial Base Pairs. (United States)

    Bätzner, Effi; Liang, Yu; Schweigert, Caroline; Unterreiner, Andreas-Neil; Wagenknecht, Hans-Achim


    The C-nucleoside based on the hydroxyquinoline ligand (Hq) is complementary to itself and forms stable Hq-Hq pairs in double-stranded DNA. These artificial Hq-Hq pairs may serve as artificial electron carriers for long-range photoinduced electron transfer in DNA, as elucidated by a combination of gel electrophoretic analysis of irradiated samples and time-resolved transient absorption spectroscopy. For this study, the Hq-Hq pair was combined with a DNA-based donor-acceptor system consisting of 6-N,N-dimethylaminopyrene conjugated to 2'-deoxyuridine as photoinducible electron donor, and methyl viologen attached to the 2'-position of uridine as electron acceptor. The Hq radical anion was identified in the time-resolved measurements and strand cleavage products support its role as an intermediate charge carrier. Hence, the Hq-Hq pair significantly enhances the electron hopping capability of DNA compared to natural DNA bases over long distances while keeping the self-assembly properties as the most attractive feature of DNA as a supramolecular architecture. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Strain dependent UV degradation of Escherichia coli DNA monitored by Fourier transform infrared spectroscopy. (United States)

    Muntean, Cristina M; Lapusan, Alexandra; Mihaiu, Liora; Stefan, Razvan


    In this work we present a method for detection of DNA isolated from nonpathogenic Escherichia coli strains, respectively. Untreated and UV irradiated bacterial DNAs were analyzed by FT-IR spectroscopy, to investigate their screening characteristic features and their structural radiotolerance at 253.7nm. FT-IR spectra, providing a high molecular structural information, have been analyzed in the wavenumber range 800-1800cm(-1). FT-IR signatures, spectroscopic band assignments and structural interpretations of these DNAs are reported. Also, UV damage at the DNA molecular level is of interest. Strain dependent UV degradation of DNA from E. coli has been observed. Particularly, alterations in nucleic acid bases, base pairing and base stacking have been found. Also changes in the DNA conformation and deoxyribose were detected. Based on this work, specific E. coli DNA-ligand interactions, drug development and vaccine design for a better understanding of the infection mechanism caused by an interference between pathogenic and nonpathogenic bacteria and for a better control of disease, respectively, might be further investigated using Fourier transform infrared spectroscopy. Besides, understanding the pathways for UV damaged DNA response, like nucleic acids repair mechanisms is appreciated.

  5. Difficulties of sex determination from forensic bone degraded DNA: A comparison of three methods. (United States)

    Quincey, Danielle; Carle, Georges; Alunni, Véronique; Quatrehomme, Gérald


    Sex determination is of paramount importance in forensic anthropology. Numerous anthropological methods have been described, including visual assessments and various measurements of bones. Nevertheless, whatever the method used, the percentage of correct classification of a single bone usually varies between 80% and 95%, due to significant intra- and inter-population variations, and sometimes variations coming from secular trends. DNA is increasingly used in a forensic context. But forensic DNA extraction from bone raises several issues, because the samples are very often badly altered and/or in very small quantity. Nuclear DNA is difficult to get from degraded samples, according to low copy number, at least in comparison with mitochondrial DNA. In a forensic context (as in a paeleoanthropological context) DNA sex determination is usually complicated by the weak amount of DNA, the degraded nature of nucleic acids, the presence of enzymatic inhibitors in DNA extracts, the possible faint amplification of Y band and the risk of contamination during either excavation or manipulation of samples. The aim of this work was to compare three methods of DNA sex determination from bones: procedure #1 using a single PCR amplification, procedure #2 using a double PCR amplification, and procedure #3 adding bleaching for decontamination of the bone, instead of simply rubbing the bone. These processes were applied to samples of bones (49 samples coming from 39 individuals) that were in various states of post mortem alteration. The main results are the following. (i) No DNA could be extracted from three skulls (parietal bones, mastoid process), the compact bone of one rib, and the diaphysis of one femur; (ii) there was a contamination in three skulls; and (iii) the Y band did not appear in two male cases, with one of the three procedures (male tibia, procedure #2) and with procedures #2 and #3 (male femur). This study emphasises the main issue while working with altered bones: the

  6. Biomedical, Artificial Intelligence, and DNA Computing Photonics Applications and Web Engineering, Wilga, May 2012 (United States)

    Romaniuk, Ryszard S.


    This paper is the fifth part (out of five) of the research survey of WILGA Symposium work, May 2012 Edition, concerned with Biomedical, Artificial Intelligence and DNA Computing technologies. It presents a digest of chosen technical work results shown by young researchers from different technical universities from this country during the Jubilee XXXth SPIE-IEEE Wilga 2012, May Edition, symposium on Photonics and Web Engineering. Topical tracks of the symposium embraced, among others, nanomaterials and nanotechnologies for photonics, sensory and nonlinear optical fibers, object oriented design of hardware, photonic metrology, optoelectronics and photonics applications, photonics-electronics co-design, optoelectronic and electronic systems for astronomy and high energy physics experiments, JET tokamak and pi-of-the sky experiments development. The symposium is an annual summary in the development of numerable Ph.D. theses carried out in this country in the area of advanced electronic and photonic systems. It is also a great occasion for SPIE, IEEE, OSA and PSP students to meet together in a large group spanning the whole country with guests from this part of Europe. A digest of Wilga references is presented [1-270].

  7. DNA-based stable isotope probing coupled with cultivation methods implicates Methylophaga in hydrocarbon degradation.

    Directory of Open Access Journals (Sweden)

    Sara eMishamandani


    Full Text Available Marine hydrocarbon-degrading bacteria perform a fundamental role in the oxidation and ultimate removal of crude oil and its petrochemical derivatives in coastal and open ocean environments. Those with an almost exclusive ability to utilize hydrocarbons as a sole carbon and energy source have been found confined to just a few genera. Here we used stable isotope probing (SIP, a valuable tool to link the phylogeny and function of targeted microbial groups, to investigate hydrocarbon-degrading bacteria in coastal North Carolina sea water (Beaufort Inlet, USA with uniformly labeled [13C]n-hexadecane. The dominant sequences in clone libraries constructed from 13C-enriched bacterial DNA (from n-hexadecane enrichments were identified to belong to the genus Alcanivorax, with ≤98% sequence identity to the closest type strain – thus representing a putative novel phylogenetic taxon within this genus. Unexpectedly, we also identified 13C-enriched sequences in heavy DNA fractions that were affiliated to the genus Methylophaga. This is a contentious group since, though some of its members have been proposed to degrade hydrocarbons, substantive evidence has not previously confirmed this. We used quantitative PCR primers targeting the 16S rRNA gene of the SIP-identified Alcanivorax and Methylophaga to determine their abundance in incubations amended with unlabeled n-hexadecane. Both showed substantial increases in gene copy number during the experiments. Subsequently, we isolated a strain representing the SIP-identified Methylophaga sequences (99.9% 16S rRNA gene sequence identity and used it to show, for the first time, direct evidence of hydrocarbon degradation by a cultured Methylophaga sp. This study demonstrates the value of coupling SIP with cultivation methods to identify and expand on the known diversity of hydrocarbon-degrading bacteria in the marine environment.

  8. [Degradation of biomolecules: a comparative study of diagenesis of DNA and proteins in human bone tissue]. (United States)

    Harbeck, Michaela; Ritz-Timme, Stefanie; Schröder, Inge; Oehmichen, Manfred; von Wurmb-Schwark, Nicole


    Diagenesis of macromolecules is a not yet fully understood process that can be important for anthropological and forensic research. Trying to elucidate the diagenesis of DNA and proteins we investigated the process of fragmentation of DNA and razemisation of aspartic acid in human bone material. We created an in vitro-model of accelerated aging by incubating bone samples in hot water. A comparison of diagenesis of molecules in those artificially aged samples with altogether 30 historical bones from different regions and of different ages was carried out. The in vitro-model showed the expected positive correlation between the increase of razemisation of aspartic acid and DNA fragmentation, while there was a much lesser correlation when investigating historical bones. The in vitro-model showed the expected correlation between the increase of razemisation of aspartic acid and DNA fragmentation and to a much lesser extent in historical bones. This study shows that diagenesis is probably influenced by additional forces affecting different macromolecules in different ways.

  9. Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation (United States)

    Ponnuswamy, Nandhini; Bastings, Maartje M. C.; Nathwani, Bhavik; Ryu, Ju Hee; Chou, Leo Y. T.; Vinther, Mathias; Li, Weiwei Aileen; Anastassacos, Frances M.; Mooney, David J.; Shih, William M.


    DNA nanostructures have evoked great interest as potential therapeutics and diagnostics due to ease and robustness of programming their shapes, site-specific functionalizations and responsive behaviours. However, their utility in biological fluids can be compromised through denaturation induced by physiological salt concentrations and degradation mediated by nucleases. Here we demonstrate that DNA nanostructures coated by oligolysines to 0.5:1 N:P (ratio of nitrogen in lysine to phosphorus in DNA), are stable in low salt and up to tenfold more resistant to DNase I digestion than when uncoated. Higher N:P ratios can lead to aggregation, but this can be circumvented by coating instead with an oligolysine-PEG copolymer, enabling up to a 1,000-fold protection against digestion by serum nucleases. Oligolysine-PEG-stabilized DNA nanostructures survive uptake into endosomal compartments and, in a mouse model, exhibit a modest increase in pharmacokinetic bioavailability. Thus, oligolysine-PEG is a one-step, structure-independent approach that provides low-cost and effective protection of DNA nanostructures for in vivo applications.

  10. DNA damage accumulation and TRF2 degradation in atypical Werner syndrome fibroblasts with LMNA mutations. (United States)

    Saha, Bidisha; Zitnik, Galynn; Johnson, Simon; Nguyen, Quyen; Risques, Rosa A; Martin, George M; Oshima, Junko


    Segmental progeroid syndromes are groups of disorders with multiple features suggestive of accelerated aging. One subset of adult-onset progeroid syndromes, referred to as atypical Werner syndrome, is caused by mutations in the LMNA gene, which encodes a class of nuclear intermediate filaments, lamin A/C. We previously described rapid telomere attrition and accelerated replicative senescence in cultured fibroblasts overexpressing mutant lamin A. In this study, we investigated the cellular phenotypes associated with accelerated telomere shortening in LMNA mutant primary fibroblasts. In early passage primary fibroblasts with R133L or L140R LMNA mutations, shelterin protein components were already reduced while cells still retained telomere lengths comparable to those of controls. There was a significant inverse correlation between the degree of abnormal nuclear morphology and the level of TRF2, a shelterin subunit, suggesting a potential causal relationship. Stabilization of the telomeres via the introduction of the catalytic subunit of human telomerase, hTERT (human telomerase reverse transcriptase), did not prevent degradation of shelterin components, indicating that reduced TRF2 in LMNA mutants is not mediated by short telomeres. Interestingly, γ-H2AX foci (reflecting double strand DNA damage) in early passage LMNA mutant primary fibroblasts and LMNA mutant hTERT fibroblasts were markedly increased in non-telomeric regions of DNA. Our results raise the possibility that mutant lamin A/C causes global genomic instability with accumulation of non-telomeric DNA damage as an early event, followed by TRF2 degradation and telomere shortening.

  11. Degradation of DNA in Haemophilus influenzae cells after x-ray irradiation. II. Comparison with theoretical models

    Energy Technology Data Exchange (ETDEWEB)

    Randolph, M.L.


    Models of the kinetics of degradation of DNA in bacterial cells following exposure to x-rays are developed and tested using data obtained with various strains of Haemophilus influenzae cells. Different mathematical models allow for different initial distributions of DNA lengths, depending on cell phase and assumed replication model, and for unilateral or bilateral degradation from initiation points, which are taken as single-strand breaks. In order to explain the observed magnitude and time course of degradation an interruption-of-degradation probability, which may be interpreted as the result of an x-ray inducible inhibitor, is introduced. Interruption of degradation is interpreted as an early and essential, but not necessarily sufficient, step for repair of DNA. Empirical best fits to the kinetic data were obtained by iterative calculation methods based on varying the rate parameters. Depending somewhat on the strain and cell phase, the data seem best described by assuming bilateral degradation, perhaps at different rates, whose total for log phase wild-type cells is roughly 5 x 10/sup 3/ nucleotides/min and an interruption rate of about 0.03/min. For stationary phase the total degradation rate is greater and the probability of degradation unchanged. Differences in the kinetics between strains are discussed briefly.

  12. Unraveling the degradation of artificial amide bonds in nylon oligomer hydrolase: from induced-fit to acylation processes. (United States)

    Baba, Takeshi; Boero, Mauro; Kamiya, Katsumasa; Ando, Hiroyuki; Negoro, Seiji; Nakano, Masayoshi; Shigeta, Yasuteru


    To elucidate how the nylon oligomer hydrolase (NylB) acquires its peculiar degradation activity towards non-biological amide bonds, we inspected the underlying enzymatic processes going from the induced-fit upon substrate binding to acylation. Specifically we investigated the mutational effects of two mutants, Y170F and D181G, indicated in former experiments as crucial systems because of their specific amino acid residues. Therefore, by adopting first-principles molecular dynamics complemented with metadynamics we provide a detailed insight into the underlying acylation mechanism. Our results show that while in the wild type (WT) the Tyr170 residue points the NH group towards the proton-acceptor site of an artificial amide bond, hence ready to react, in the Y170F this does not occur. The reason is ascribed to the absence of Tyr170 in the mutant, which is replaced by phenylalanine, which is unable to form hydrogen bond with the amide bond; thus, resulting in an increase in the activation barrier of more than 10 kcal mol(-1). Nonetheless, despite the lack of hydrogen bonding between the Y170F and the substrate, the highest free energy barrier for the induced-fit is similar to that of WT. This seems to suggest that in the induced-fit process, kinetics is little affected by the mutation. On the basis of additional structural homology analyses on the enzymes of the same family, we suggest that natural selection is responsible for the development of the peculiar hydrolytic activity of Arthrobacter sp. KI72.

  13. Assessment of DNA degradation induced by thermal and UV radiation processing: implications for quantification of genetically modified organisms. (United States)

    Ballari, Rajashekhar V; Martin, Asha


    DNA quality is an important parameter for the detection and quantification of genetically modified organisms (GMO's) using the polymerase chain reaction (PCR). Food processing leads to degradation of DNA, which may impair GMO detection and quantification. This study evaluated the effect of various processing treatments such as heating, baking, microwaving, autoclaving and ultraviolet (UV) irradiation on the relative transgenic content of MON 810 maize using pRSETMON-02, a dual target plasmid as a model system. Amongst all the processing treatments examined, autoclaving and UV irradiation resulted in the least recovery of the transgenic (CaMV 35S promoter) and taxon-specific (zein) target DNA sequences. Although a profound impact on DNA degradation was seen during the processing, DNA could still be reliably quantified by Real-time PCR. The measured mean DNA copy number ratios of the processed samples were in agreement with the expected values. Our study confirms the premise that the final analytical value assigned to a particular sample is independent of the degree of DNA degradation since the transgenic and the taxon-specific target sequences possessing approximately similar lengths degrade in parallel. The results of our study demonstrate that food processing does not alter the relative quantification of the transgenic content provided the quantitative assays target shorter amplicons and the difference in the amplicon size between the transgenic and taxon-specific genes is minimal.

  14. Degradable polymer-coated gold nanoparticles for co-delivery of DNA and siRNA. (United States)

    Bishop, Corey J; Tzeng, Stephany Y; Green, Jordan J


    Gold nanoparticles have utility for in vitro, ex vivo and in vivo imaging applications as well as for serving as a scaffold for therapeutic delivery and theranostic applications. Starting with gold nanoparticles as a core, layer-by-layer degradable polymer coatings enable the simultaneous co-delivery of DNA and short interfering RNA (siRNA). To engineer release kinetics, polymers which degrade through two different mechanisms can be utilized to construct hybrid inorganic/polymeric particles. During fabrication of the nanoparticles, the zeta potential reverses upon the addition of each oppositely charged polyelectrolyte layer and the final nanoparticle size reaches approximately 200nm in diameter. When the hybrid gold/polymer/nucleic acid nanoparticles are added to human primary brain cancer cells in vitro, they are internalizable by cells and reach the cytoplasm and nucleus as visualized by transmission electron microscopy and observed through exogenous gene expression. This nanoparticle delivery leads to both exogenous DNA expression and siRNA-mediated knockdown, with the knockdown efficacy superior to that of Lipofectamine® 2000, a commercially available transfection reagent. These gold/polymer/nucleic acid hybrid nanoparticles are an enabling theranostic platform technology capable of delivering combinations of genetic therapies to human cells.

  15. DNA-SIP identifies sulfate-reducing Clostridia as important toluene degraders in tar-oil-contaminated aquifer sediment

    Energy Technology Data Exchange (ETDEWEB)

    Winderl, C.; Penning, H.; von Netzer, F.; Meckenstock, R.U.; Lueders, T. [Helmholtz Zentrum Munchen, Neuherberg (Germany)


    Global groundwater resources are constantly challenged by a multitude of contaminants such as aromatic hydrocarbons. Especially in anaerobic habitats, a large diversity of unrecognized microbial populations may be responsible for their degradation. Still, our present understanding of the respective microbiota and their ecophysiology is almost exclusively based on a small number of cultured organisms, mostly within the Proteobacteria. Here, by DNA-based stable isotope probing (SIP), we directly identified the most active sulfate-reducing toluene degraders in a diverse sedimentary microbial community originating from a tar-oil-contaminated aquifer at a former coal gasification plant. On incubation of fresh sediments with {sup 13}C{sub 7}-toluene, the production of both sulfide and (CS{sub 2}){sup 13}CO{sub 2} was clearly coupled to the {sup 13}Clabeling of DNA of microbes related to Desulfosporosinus spp. within the Peptococcaceae (Clostridia). The screening of labeled DNA fractions also suggested a novel benzylsuccinate synthase alpha-subunit (bssA) sequence type previously only detected in the environment to be tentatively affiliated with these degraders. However, carbon flow from the contaminant into degrader DNA was only similar to 50%, pointing toward high ratios of heterotrophic CS{sub 2}-fixation during assimilation of acetyl-CoA originating from the contaminant by these degraders. These findings demonstrate that the importance of non-proteobacterial populations in anaerobic aromatics degradation, as well as their specific ecophysiology in the subsurface may still be largely ungrasped.

  16. Serum-induced degradation of 3D DNA box origami observed with high-speed atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    Zaixing Jiang[1,2,3; Shuai Zhang[2,3; Chuanxu Yang[2; Jorgen Kjems[2; Yudong Huang[1; Flemming Besenbacher[2; Mingdong Dong[2


    3D DNA origami holds tremendous potential for the encapsulation and selective release of therapeutic drugs. Observations of the real-time performance of these structures in physiological environments will contribute to the development of future applications. We investigated the degradation kinetics of 3D DNA box origami in serum by using high-speed atomic force microscope optimized for imaging 3D DNA origami in real time. The time resolution allowed to characterize the stages of serum effects on individual 3D DNA boxes origami with nanometer resolution. Our results indicate that the digestion process is a combination of rapid collapse and slow degradation phases. Damage to box origami occurs mainly in the collapse phase. Thus, the structural stability of 3D DNA box origami should be improved, especially in the collapse phase, before these structures are used in clinical applications.

  17. Inhibition of proteasomal degradation of rpn4 impairs nonhomologous end-joining repair of DNA double-strand breaks.

    Directory of Open Access Journals (Sweden)

    Donghong Ju

    Full Text Available BACKGROUND: The proteasome homeostasis in Saccharomyces cerevisiae is regulated by a negative feedback circuit in which the transcription factor Rpn4 induces the proteasome genes and is rapidly degraded by the assembled proteasome. The integrity of the Rpn4-proteasome feedback loop is critical for cell viability under stressed conditions. We have demonstrated that inhibition of Rpn4 degradation sensitizes cells to DNA damage, particularly in response to high doses of DNA damaging agents. The underlying mechanism, however, remains unclear. METHODOLOGY/PRINCIPAL FINDINGS: Using yeast genetics and biochemical approach we show that inhibition of Rpn4 degradation displays a synthetic growth defect with deletion of the MEC1 checkpoint gene and sensitizes several checkpoint mutants to DNA damage. In addition, inhibition of Rpn4 degradation leads to a defect in repair of double-strand breaks (DSBs by nonhomologous end-joining (NHEJ. The expression levels of several key NHEJ genes are downregulated and the recruitment of Yku70 to a DSB is reduced by inhibition of Rpn4 degradation. We find that Rpn4 and the proteasome are recruited to a DSB, suggesting their direct participation in NHEJ. Inhibition of Rpn4 degradation may result in a concomitant delay of release of Rpn4 and the proteasome from a DSB. CONCLUSION/SIGNIFICANCE: This study provides the first evidence for the role of proteasomal degradation of Rpn4 in NHEJ.

  18. Multiple DNA Extractions Coupled with Stable-Isotope Probing of Anthracene-Degrading Bacteria in Contaminated Soil▿† (United States)

    Jones, Maiysha D.; Singleton, David R.; Sun, Wei; Aitken, Michael D.


    In many of the DNA-based stable-isotope probing (SIP) studies published to date in which soil communities were investigated, a single DNA extraction was performed on the soil sample, usually using a commercial DNA extraction kit, prior to recovering the 13C-labeled (heavy) DNA by density-gradient ultracentrifugation. Recent evidence suggests, however, that a single extraction of a soil sample may not lead to representative recovery of DNA from all of the organisms in the sample. To determine whether multiple DNA extractions would affect the DNA yield, the eubacterial 16S rRNA gene copy number, or the identification of anthracene-degrading bacteria, we performed seven successive DNA extractions on the same aliquot of contaminated soil either untreated or enriched with [U-13C]anthracene. Multiple extractions were necessary to maximize the DNA yield and 16S rRNA gene copy number from both untreated and anthracene-enriched soil samples. Sequences within the order Sphingomonadales, but unrelated to any previously described genus, dominated the 16S rRNA gene clone libraries derived from 13C-enriched DNA and were designated “anthracene group 1.” Sequences clustering with Variovorax spp., which were also highly represented, and sequences related to the genus Pigmentiphaga were newly associated with anthracene degradation. The bacterial groups collectively identified across all seven extracts were all recovered in the first extract, although quantitative PCR analysis of SIP-identified groups revealed quantitative differences in extraction patterns. These results suggest that performing multiple DNA extractions on soil samples improves the extractable DNA yield and the number of quantifiable eubacterial 16S rRNA gene copies but have little qualitative effect on the identification of the bacterial groups associated with the degradation of a given carbon source by SIP. PMID:21398486

  19. Multiple DNA extractions coupled with stable-isotope probing of anthracene-degrading bacteria in contaminated soil. (United States)

    Jones, Maiysha D; Singleton, David R; Sun, Wei; Aitken, Michael D


    In many of the DNA-based stable-isotope probing (SIP) studies published to date in which soil communities were investigated, a single DNA extraction was performed on the soil sample, usually using a commercial DNA extraction kit, prior to recovering the (13)C-labeled (heavy) DNA by density-gradient ultracentrifugation. Recent evidence suggests, however, that a single extraction of a soil sample may not lead to representative recovery of DNA from all of the organisms in the sample. To determine whether multiple DNA extractions would affect the DNA yield, the eubacterial 16S rRNA gene copy number, or the identification of anthracene-degrading bacteria, we performed seven successive DNA extractions on the same aliquot of contaminated soil either untreated or enriched with [U-(13)C]anthracene. Multiple extractions were necessary to maximize the DNA yield and 16S rRNA gene copy number from both untreated and anthracene-enriched soil samples. Sequences within the order Sphingomonadales, but unrelated to any previously described genus, dominated the 16S rRNA gene clone libraries derived from (13)C-enriched DNA and were designated "anthracene group 1." Sequences clustering with Variovorax spp., which were also highly represented, and sequences related to the genus Pigmentiphaga were newly associated with anthracene degradation. The bacterial groups collectively identified across all seven extracts were all recovered in the first extract, although quantitative PCR analysis of SIP-identified groups revealed quantitative differences in extraction patterns. These results suggest that performing multiple DNA extractions on soil samples improves the extractable DNA yield and the number of quantifiable eubacterial 16S rRNA gene copies but have little qualitative effect on the identification of the bacterial groups associated with the degradation of a given carbon source by SIP.

  20. Fluorescence formation from the interaction of DNA with lipid oxidation degradation products. (United States)

    Frankel, E N; Neff, W E; Brooks, D D; Fujimoto, K


    To clarify the mechanism of fluorescence formation between DNA and lipid degradation products in the presence of ferric chloride and ascorbic acid, a number of carbonyl compounds and decomposition products of pure methyl linolenate hydroperoxides were examined. Keto derivatives of methyl ricinoleate, linoleate, and oleate, alkanals and 2-alkenals produced little or no fluorescence with DNA in the presence of ferric chloride-ascorbic acid. 2,4-Alkadienals were more active and 2,4,7-decatrienal was the most active. Mixtures of volatile aldehydes prepared from linolenate hydroperoxide decomposed either thermally or with iron and ascorbate had the same activity as 2,4,7-decatrienal. Higher molecular-weight products from the decomposition of methyl linolenate hydroperoxides showed relatively low activity. beta-Carotene, alpha-tocopherol and other antioxidants effectively reduced the amount of fluorescence formed by linolenate hydroperoxides. The results suggest that, in addition to hydroperoxide decomposition products, singlet oxygen and/or free radical species contribute significantly to the fluorescence formed from the interaction of methyl linolenate hydroperoxides with DNA in the presence of ferric chloride and ascorbic acid.

  1. DNA degradation by aqueous extract of Aloe vera in the presence of copper ions. (United States)

    Naqvi, Shoa; Ullah, M F; Hadi, S M


    The plant Aloe vera has long been used in medicine, as dietary supplements and for cosmetic purposes. Aloe vera extracts are a rich source of polyphenols, such as aloin and aloe emodin and have shown a wide range of pharmacological properties, including anti-inflammatory and anti-cancer properties. The bioactive component aloe emodin has been reported to induce apoptosis in various cancer cell lines. Many of the biological activities of Aloe vera have been attributed to its antioxidant properties. However, most plant-derived polyphenols that are also present in Aloe vera may exhibit pro-oxidant properties either alone or in the presence of transition metals, such as copper. Previous reports from this laboratory have implicated the pro-oxidant action as one of the mechanisms for their anti-cancer properties. In the present paper, we show that aqueous extract of Aloe vera is also able to cause DNA degradation in the presence of copper ions. Further, the extract is also able to reduce Cu(II) to Cu(I) and generate reactive oxygen species, such as superoxide anion and hydroxyl radicals in a dose-dependent manner, which correlates with ability of the extract to cause DNA breakage. Thus, the study shows that in addition to antioxidant activity, Aloe vera extract also possess pro-oxidant properties, leading to oxidative DNA breakage.

  2. Nanobiosensor for Detection and Quantification of DNA Sequences in Degraded Mixed Meats

    Directory of Open Access Journals (Sweden)

    M. E. Ali


    Full Text Available A novel class of nanobiosensor was developed by integrating a 27-nucleotide AluI fragment of swine cytochrome b (cytb gene to a 3-nm diameter citrate-tannate coated gold nanoparticle (GNP. The biosensor detected 0.5% and 1% pork in raw and 2.5-h autoclaved pork-beef binary admixtures in a single step without any separation or washing. The hybridization kinetics of the hybrid sensor was studied with synthetic and AluI digested real pork targets from moderate to extreme target concentrations and a sigmoidal relationship was found. Using the kinetic curve, a convenient method for quantifying and counting target DNA copy number was developed. The accuracy of the method was over 90% and 80% for raw and autoclaved pork-beef binary admixtures in the range of 5–100% pork adulteration. The biosensor probe identified a target DNA sequence that was several-folds shorter than a typical PCR-template. This offered the detection and quantitation of potential targets in highly processed or degraded samples where PCR amplification was not possible due to template crisis. The assay was a viable alternative approach of qPCR for detecting, quantifying and counting copy number of shorter size DNA sequences to address a wide ranging biological problem in food industry, diagnostic laboratories and forensic medicine.

  3. Degradation of paternal mitochondria after fertilization: implications for heteroplasmy, assisted reproductive technologies and mtDNA inheritance. (United States)

    Sutovsky, Peter; Van Leyen, Klaus; McCauley, Tod; Day, Billy N; Sutovsky, Miriam


    Maternal inheritance of mitochondrial DNA has long been regarded as a major paradox in developmental biology. While some confusion may still persist in popular science, research data clearly document that the paternal sperm-borne mitochondria of most mammalian species enter the ooplasm at fertilization and are specifically targeted for degradation by the resident ubiquitin system. Ubiquitin is a proteolytic chaperone that forms covalently linked polyubiquitin chains on the targeted proteinaceous substrates. The polyubiquitin tag redirects the substrate proteins to a 26-S proteasome, a multi-subunit proteolytic organelle. Thus, specific proteasomal inhibitors reversibly block sperm mitochondrial degradation in ooplasm. Lysosomal degradation and the activity of membrane-lipoperoxidating enzyme 15-lipoxygenase (15-LOX) may also contribute to sperm mitochondrial degradation in the ooplasm, but probably is not crucial. Prohibitin, the major protein of the inner mitochondrial membrane, appears to be ubiquitinated in the sperm mitochondria. Occasional occurrence of paternal inheritance of mtDNA has been suggested in mammals including humans. While most such evidence has been widely disputed, it warrants further examination. Of particular concern is the documented heteroplasmy, i.e. mixed mtDNA inheritance after ooplasmic transplantation. Intracytoplasmic sperm injection (ICSI) has inherent potential for delaying the degradation of sperm mitochondria. However, paternal mtDNA inheritance after ICSI has not been documented so far.

  4. Synthesis, spectral characterization and eukaryotic DNA degradation of thiosemicarbazones and their platinum(IV) complexes (United States)

    Al-Hazmi, G. A.; El-Metwally, N. M.; El-Gammal, O. A.; El-Asmy, A. A.


    The condensation products of acetophenone (or its derivatives), salicylaldehyde and o-hydroxy- p-methoxybenzophenone with thiosemicarbazide and ethyl- or phenyl-thiosemicarbazide are the investigated thiosemicarbazones. Their reactions with H 2PtCl 6 produced Pt(IV) complexes characterized by elemental, thermal, mass, IR and electronic spectral studies. The coordination modes were found mononegative bidentate in the acetophenone derivatives and binegative tridentate in the salicylaldehyde derivatives. The complexes were analyzed thermogravimetrically and found highly stable. Some ligands and their complexes were screened against Sarcina sp. and E. coli using the cup-diffusion technique. [Pt( oHAT)(OH)Cl] shows higher activity against E. coli than the other compounds. The degradation power of the tested compounds on the calf thymus DNA supports their selectivity against bacteria and not against the human or related eukaryotic organisms.

  5. Modification of bacterial artificial chromosomes (BACs) and preparation of intact BAC DNA for generation of transgenic mice. (United States)

    Gong, Shiaoching; Yang, X William


    BAC transgenesis is a powerful tool for the study of gene expression and gene function in the mouse in vivo. In this unit, detailed protocols are provided for modification (i.e., marker gene insertion, deletion, or point mutation) of BACs by homologous recombination in E. coli. This method utilizes a shuttle vector that allows transient expression of the E. coli RecA gene to support homologous recombination in the BAC host bacteria. In addition, two protocols are provided for purification of BAC DNA for microinjection to generate transgenic mice. Since BAC DNA is prone to degradation, which may introduce positional effects in transgenic mice, two methods are given for purification of intact BAC DNA for subsequent microinjection.

  6. Flow cytofluorometric assay of human whole blood leukocyte DNA degradation in response to Yersinia pestis and Staphylococcus aureus (United States)

    Kravtsov, Alexander L.; Grebenyukova, Tatyana P.; Bobyleva, Elena V.; Golovko, Elena M.; Malyukova, Tatyana A.; Lyapin, Mikhail N.; Kostyukova, Tatyana A.; Yezhov, Igor N.; Kuznetsov, Oleg S.


    Human leukocytes containing less than 2C DNA per cell (damaged or dead cells) were detected and quantified by flow cytometry and DNA-specific staining with ethidium bromide and mithramycin in whole blood infected with Staphylococcus aureus or Yersinia pestis. Addition of live S. aureus to the blood (100 microbe cells per one leukocyte) resulted in rapid degradation of leukocyte DNA within 3 to 6 hours of incubation at 37 degree(s)C. However, only about 50 percent cells were damaged and the leukocytes with the intact genetic apparatus could be found in the blood for a period up to 24 hours. The leukocyte injury was preceded by an increase of DNA per cell content (as compared to the normal one) that was likely to be connected with the active phagocytosis of S. aureus by granulocytes (2C DNA of diploid phagocytes plus the all bacterial DNA absorbed). In response to the same dose of actively growing (at 37 degree(s)C) virulent Y. pestis cells, no increase in DNA content per cell could be observed in the human blood leukocytes. The process of the leukocyte DNA degradation started after a 6-hour incubation, and between 18 to 24 hours of incubation about 90 percent leukocytes (phagocytes and lymphocytes) lost their specific DNA fluorescence. These results demonstrated a high potential of flow cytometry in comparative analysis in vitro of the leukocyte DNA degradation process in human blood in response to bacteria with various pathogenic properties. They agree with the modern idea of an apoptotic mechanism of immunosuppression in plague.

  7. Integrated Model of DNA Sequence Numerical Representation and Artificial Neural Network for Human Donor and Acceptor Sites Prediction

    Directory of Open Access Journals (Sweden)

    Mohammed Abo-Zahhad


    Full Text Available Human Genome Project has led to a huge inflow of genomic data. After the completion of human genome sequencing, more and more effort is being put into identification of splicing sites of exons and introns (donor and acceptor sites. These invite bioinformatics to analysis the genome sequences and identify the location of exon and intron boundaries or in other words prediction of splicing sites. Prediction of splice sites in genic regions of DNA sequence is one of the most challenging aspects of gene structure recognition. Over the last two decades, artificial neural networks gradually became one of the essential tools in bioinformatics. In this paper artificial neural networks with different numerical mapping techniques have been employed for building integrated model for splice site prediction in genes. An artificial neural network is trained and then used to find splice sites in human genes. A comparison between different mapping methods using trained neural network in terms of their precision in prediction of donor and acceptor sites will be presented in this paper. Training and measuring performance of neural network are carried out using sequences of the human genome (GRch37/hg19- chr21. Simulation results indicate that using Electron-Ion Interaction Potential numerical mapping method with neural network yields to the best performance in prediction.

  8. DNA degradation and genetic analysis of empty puparia: genetic identification limits in forensic entomology. (United States)

    Mazzanti, Morena; Alessandrini, Federica; Tagliabracci, Adriano; Wells, Jeffrey D; Campobasso, Carlo P


    Puparial cases are common remnants of necrophagous flies in crime investigations. They usually represent the longest developmental time and, therefore, they can be very useful for the estimation of the post-mortem interval (PMI). However, before any PMI estimate, it is crucial to identify the species of fly eclosed from each puparium associated with the corpse. Morphological characteristics of the puparium are often distinctive enough to permit a species identification. But, even an accurate morphological analysis of empty puparia cannot discriminate among different species of closely related flies. Furthermore, morphological identification may be impossible if the fly puparia are poorly preserved or in fragments. This study explores the applicability of biomolecular techniques on empty puparia and their fragments for identification purposes. A total of 63 empty puparia of necrophagous Diptera resulting from forensic casework were examined. Samples were divided into three groups according to size, type and time of eclosion in order to verify whether the physical characteristics and puparia weathering can influence the amount of DNA extraction. The results suggest that a reliable genetic identification of forensically important flies may also be performed from empty puparia and/or their fragments. However, DNA degradation can deeply compromise the genetic analysis since the older the fly puparia, the smaller are the amplified fragments.

  9. Insights into the processes behind the contamination of degraded human teeth and bone samples with exogenous sources of DNA

    DEFF Research Database (Denmark)

    Gilbert, M. T. P.; Hansen, Anders J.; Willerslev, E.


    A principal problem facing human DNA studies that use old and degraded remains is contamination from other sources of human DNA. In this study we have attempted to contaminate deliberately bones and teeth sampled from a medieval collection excavated in Trondheim, Norway, in order to investigate...... and are difficult to decontaminate using the tested protocol. We believe that this is largely due to the porous nature of bone and teeth facilitating the deep penetration of the contaminant DNA. To simulate a more realistic handling situation, 27 further teeth were directly handled and washed, then decontaminated...

  10. SCFCyclin F-dependent degradation of CDC6 suppresses DNA re-replication

    DEFF Research Database (Denmark)

    Walter, David; Hoffmann, Saskia; Komseli, Eirini-Stavroula


    origin licensing, however, it is poorly understood how CDC6 activity is constrained in higher eukaryotes. Here we report that the SCF(Cyclin F) ubiquitin ligase complex prevents DNA re-replication by targeting CDC6 for proteasomal degradation late in the cell cycle. We show that CDC6 and Cyclin F...

  11. LDFF, the large molecular weight DNA fragmentation factor, is responsible for the large molecular weight DNA degradation during apoptosis in Xenopus egg extracts

    Institute of Scientific and Technical Information of China (English)

    Zhi Gang LU; Chuan Mao ZHANG; Zhong He ZHAI


    DNA degradation is a biochemical hallmark in apoptosis. It has been demonstrated in many cell types that there are two stages of DNA fragmentation during the apoptotic execution. In the early stage, chromatin DNA is cut into large molecular weight DNA fragments, although the responsible nuclease(s) has not been recognized. In the late stage, the chromatin DNA is cleaved further into short oligonucleosomal fragments by a well-characterized nuclease in apoptosis,the caspase-activated DNase (CAD/DFF40). In this study, we demonstrate that large molecular weight DNA fragmentation also occurs in Xenopus egg extracts in apoptosis. We show that the large molecular weight DNA fragmentation factor (LDFF) is not the Xenopus CAD homolog XCAD. LDFF is activated by caspase-3. The large molecular weight DNA fragmentation activity of LDFF is Mg2+-dependent and Ca2+-independent, can occur in both acidic and neutral pH conditions and can tolerate 45℃ treatment. These results indicate that LDFF in Xenopus egg extracts might be a new DNase (or DNases) responsible for the large DNA fragmentation.

  12. Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing. (United States)

    Portune, Kevin J; Pérez, M Carmen; Álvarez-Hornos, F Javier; Gabaldón, Carmen


    Microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. To further explore this relationship, 16S rDNA tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. Changes in microbial structure were observed between different stages of biofilter operation, and the level of styrene concentration was revealed to be a critical factor affecting these changes. Bacterial genera Azoarcus and Pseudomonas were among the dominant classified genera in the biofilter. Canonical correspondence analysis (CCA) and correlation analysis revealed that the genera Brevundimonas, Hydrogenophaga, and Achromobacter may play important roles in styrene degradation under increasing styrene concentrations. No significant correlations (P > 0.05) could be detected between biofilter operational/functional parameters and biodiversity measurements, although biological heterogeneity within biofilms and/or technical variability within pyrosequencing may have considerably affected these results. Percentages of selected bacterial taxonomic groups detected by fluorescence in situ hybridization (FISH) were compared to results from pyrosequencing in order to assess the effectiveness and limitations of each method for identifying each microbial taxon. Comparison of results revealed discrepancies between the two methods in the detected percentages of numerous taxonomic groups. Biases and technical limitations of both FISH and pyrosequencing, such as the binding of FISH probes to non-target microbial groups and lack of classification of sequences for defined taxonomic groups from pyrosequencing, may partially explain some differences between the two methods.

  13. The Effects of Magnesium Ions on the Enzymatic Synthesis of Ligand-Bearing Artificial DNA by Template-Independent Polymerase

    Directory of Open Access Journals (Sweden)

    Yusuke Takezawa


    Full Text Available A metal-mediated base pair, composed of two ligand-bearing nucleotides and a bridging metal ion, is one of the most promising components for developing DNA-based functional molecules. We have recently reported an enzymatic method to synthesize hydroxypyridone (H-type ligand-bearing artificial DNA strands. Terminal deoxynucleotidyl transferase (TdT, a template-independent DNA polymerase, was found to oligomerize H nucleotides to afford ligand-bearing DNAs, which were subsequently hybridized through copper-mediated base pairing (H–CuII–H. In this study, we investigated the effects of a metal cofactor, MgII ion, on the TdT-catalyzed polymerization of H nucleotides. At a high MgII concentration (10 mM, the reaction was halted after several H nucleotides were appended. In contrast, at lower MgII concentrations, H nucleotides were further appended to the H-tailed product to afford longer ligand-bearing DNA strands. An electrophoresis mobility shift assay revealed that the binding affinity of TdT to the H-tailed DNAs depends on the MgII concentration. In the presence of excess MgII ions, TdT did not bind to the H-tailed strands; thus, further elongation was impeded. This is possibly because the interaction with MgII ions caused folding of the H-tailed strands into unfavorable secondary structures. This finding provides an insight into the enzymatic synthesis of longer ligand-bearing DNA strands.

  14. Quantitative analysis of genomic DNA degradation in whole blood under various storage conditions for molecular diagnostic testing. (United States)

    Permenter, Jessalyn; Ishwar, Arjun; Rounsavall, Angie; Smith, Maddie; Faske, Jennifer; Sailey, Charles J; Alfaro, Maria P


    Proper storage of whole blood is crucial for isolating nucleic acids from leukocytes and to ensure adequate performance of downstream assays in the molecular diagnostic laboratory. Short-term and long-term storage recommendations are lacking for successful isolation of genomic DNA (gDNA). Container type (EDTA or heparin), temperature (4 °C and room temperature) and time (1-130 days) were assessed as criterion for sample acceptance policies. The percentage of integrated area (%Ti) between 150 and 10,000 bp from the 2200 TapeStation electropherogram was calculated to measure gDNA degradation. Refrigerated EDTA samples yielded gDNA with low %Ti (high quality). Heparinized samples stored at room temperature yielded gDNA of worst quality. Downstream analysis demonstrated that the quality of the gDNA correlated with the quality of the data; samples with high %Ti generated significantly lower levels of high molecular weight amplicons. Recommendations from these analyses include storing blood samples intended for nucleic acid isolation in EDTA tubes at 4 °C for long term storage (>10 days). gDNA should be extracted within 3 days when blood is stored at room temperature regardless of the container. Finally, refrigerated heparinized samples should not be stored longer than 9 days if expecting high quality gDNA isolates. Laboratories should consider many factors, in addition to the results obtained herein, to update their policies for sample acceptance for gDNA extraction intended for molecular genetic testing.

  15. Cell wall degrading isoenzyme profiles of Trichoderma biocontrol strains show correlation with rDNA species

    Institute of Scientific and Technical Information of China (English)

    Sanz L; Hermosa M R; González F J; Monte E


    @@ Species of the fungus Trichoderma, a genus of Hyphomycetes, are ubiquitous in the environment, but especially in soil. They have been used in a wide range of commercial applications including the production of hydrolases and in the biological control of plant diseases. A fundamental part of the Trichoderma antifungal system consists of a series of genes coding for a surprising variety of extracellular cell wall degrading enzymes (CWDE).Characterisation and identification of strains at the species level is the first step in utilizing the full potential of fungi in specific applications. One aim when isolating Trichoderma strains is to identify those which can be used in new agricultural and industrial applications. In the past it was not uncommon that biocontrol strains were defined as T. harzianum Rifai, due to the limited classification system of the genus Trichoderma. In recent years, several PCR-based molecular techniques have been used to detect and discriminate among microorganisms. Sequence analysis of the ITS regions of the ribosomal DNA and gene fragments as those corresponding to tef1 gene have been helpful in the neotypification, description and characterization of species in the genus Trichoderna.Another useful method for the identification of Trichoderma strains is the randomly amplified polymorphic DNA (RAPD) technique.Isozyme polymorphisms evaluation of five putative extracellular lytic enzymes loci (β-1,3-glucanase, β-1,6-glucanase, cellulase, chitinase and protease antivities) were carried out using representative strains of defined molecular groups. CWDE groupings obtained from biocontrol strains are discussed in relation to their phylogenetic location and antifungal activities.Compiling morphological, biochemical and sequence information data into a common database would provide a useful resource that could be used to accurately name new haplotypes identified in the future and correctly place them within the genus Trichoderma.

  16. A 6. 5-Mb yeast artificial chromosome contig incorporating 33 DNA markers on the human X chromosome at Xq22

    Energy Technology Data Exchange (ETDEWEB)

    Vetrie, D.; Kendall, E.; Coffey, A.; Hassock, S.; Collins, J.; Todd, C.; Bobrow, M.; Bentley, D.R. (Paediatric Research Unit, London (United Kingdom)); Lehrach, H. (Imperial Cancer Research Fund, London (United Kingdom)); Harris, A. (John Radcliffe Hospital, Oxford (United Kingdom))


    The Xq22 region of the human X chromosome contains genes for a number of inherited disorders. Sixty-nine yeast artificial chromosome clones have been isolated and assembled into a 6.5-Mb contig that contains 33 DNA markers localized to this region. This contig extends distally from DXS366 to beyond DXS87 and includes the genes involved in X-linked agammaglobulinemia (btk), Fabry disease (GLA), and Pelizaeus-Merzbacher disease (PLP). The order of markers in this contig is consistent with the known genetic and physical mapping information of Xq22. This cloned material provides a source from which to isolate other genes located in this part of the X chromosome. 45 refs., 2 figs., 2 tabs.

  17. Comparison of three different DNA extraction methods from a highly degraded biological material. (United States)

    Kuś, M; Ossowski, A; Zielińska, G


    The identification of unknown victims is one of the most challenging tasks faced by forensic medicine. This is due to the rapid decomposition of tissues, beginning at the moment of death and caused by released enzymes and microbial activity. Decay is directly associated with the decomposition of soft tissues and also the degradation of genetic material inside cells. Decomposition rates vary depending on a number of environmental factors, including temperature, humidity, season, and soil properties. Decomposition also differs between bodies left in the open air or buried. To date, forensic medicine has identified mainly people who were the victims of various types of criminal offences. However, with advances in identification methods, increasingly frequent attempts are made to identify the victims of armed conflicts, crimes of totalitarian regimes, or genocide. The aim of the study was to compare three different methods for the extraction of nuclear DNA from material considered in forensic medicine as difficult to handle, i.e. fragments of bones and teeth, and to determine the performance of these methods and their suitability for identification procedures. Copyright © 2016 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  18. Statistical optimization and artificial neural network modeling for acridine orange dye degradation using in-situ synthesized polymer capped ZnO nanoparticles. (United States)

    Dhiman, Nitesh; Markandeya; Singh, Amrita; Verma, Neeraj K; Ajaria, Nidhi; Patnaik, Satyakam


    ZnO NPs were synthesized by a prudent green chemistry approach in presence of polyacrylamide grafted guar gum polymer (pAAm-g-GG) to ensure uniform morphology, and functionality and appraised for their ability to degrade photocatalytically Acridine Orange (AO) dye. These ZnO@pAAm-g-GG NPs were thoroughly characterized by various spectroscopic, XRD and electron microscopic techniques. The relative quantity of ZnO NPs in polymeric matrix has been estimated by spectro-analytical procedure; AAS and TGA analysis. The impact of process parameters viz. NP's dose, contact time and AO dye concentration on percentage photocatalytic degradation of AO dyes were evaluated using multivariate optimizing tools, Response Surface Methodology (RSM) involving Box-Behnken Design (BBD) and Artificial Neural Network (ANN). Congruity of the BBD statistical model was implied by R(2) value 0.9786 and F-value 35.48. At RSM predicted optimal condition viz. ZnO@pAAm-g-GG NP's dose of 0.2g/L, contact time of 210min and AO dye concentration 10mg/L, a maximum of 98% dye degradation was obtained. ANOVA indicated appropriateness of the model for dye degradation owing to "Prob.>F" less than 0.05 for variable parameters. We further, employed three layers feed forward ANN model for validating the BBD process parameters and suitability of our chosen model. The evaluation of Levenberg-Marquardt algorithm (ANN1) and Gradient Descent with adaptive learning rate (ANN2) model employed to scrutinize the best method and found experimental values of AO dye degradation were in close to those with predicated value of ANN 2 modeling with minimum error.

  19. Interaction of a copper (II) complex containing an artificial sweetener (aspartame) with calf thymus DNA. (United States)

    Shahabadi, Nahid; Khodaei, Mohammad Mehdi; Kashanian, Soheila; Kheirdoosh, Fahimeh


    A copper (II) complex containing aspartame (APM) as ligand, Cu(APM)2Cl2⋅2H2O, was synthesized and characterized. In vitro binding interaction of this complex with native calf thymus DNA (CT-DNA) was studied at physiological pH. The interaction was studied using different methods: spectrophotometric, spectrofluorometric, competition experiment, circular dichroism (CD) and viscosimetric techniques. Hyperchromicity was observed in UV absorption band of Cu(APM)2Cl2⋅2H2O. A strong fluorescence quenching reaction of DNA to Cu(APM)2Cl2⋅2H2O was observed and the binding constants (Kf) and corresponding numbers of binding sites (n) were calculated at different temperatures. Thermodynamic parameters, enthalpy change (ΔH) and entropy change (ΔS) were calculated to be+89.3 kJ mol(-1) and+379.3 J mol(-1) K(-1) according to Van't Hoff equation which indicated that reaction is predominantly entropically driven. Experimental results from spectroscopic methods were comparable and further supported by viscosity measurements. We suggest that Cu(APM)2Cl2⋅2H2O interacts with calf thymus DNA via a groove interaction mode with an intrinsic binding constant of 8×10+4 M(-1). Binding of this copper complex to DNA was found to be stronger compared to aspartame which was studied recently.

  20. Autophagic degradation of dBruce controls DNA fragmentation in nurse cells during late Drosophila melanogaster oogenesis (United States)

    Shravage, Bhupendra V.; Sagona, Antonia P.; Lamark, Trond; Bjørkøy, Geir; Johansen, Terje; Rusten, Tor Erik; Brech, Andreas; Baehrecke, Eric H.


    Autophagy is an evolutionarily conserved pathway responsible for degradation of cytoplasmic material via the lysosome. Although autophagy has been reported to contribute to cell death, the underlying mechanisms remain largely unknown. In this study, we show that autophagy controls DNA fragmentation during late oogenesis in Drosophila melanogaster. Inhibition of autophagy by genetically removing the function of the autophagy genes atg1, atg13, and vps34 resulted in late stage egg chambers that contained persisting nurse cell nuclei without fragmented DNA and attenuation of caspase-3 cleavage. The Drosophila inhibitor of apoptosis (IAP) dBruce was found to colocalize with the autophagic marker GFP-Atg8a and accumulated in autophagy mutants. Nurse cells lacking Atg1 or Vps34 in addition to dBruce contained persisting nurse cell nuclei with fragmented DNA. This indicates that autophagic degradation of dBruce controls DNA fragmentation in nurse cells. Our results reveal autophagic degradation of an IAP as a novel mechanism of triggering cell death and thereby provide a mechanistic link between autophagy and cell death. PMID:20713604

  1. Degradation and half-life of DNA present in biomass from a genetically-modified organism during land application. (United States)

    Halter, Mathew C; Zahn, James A


    White biotechnology has made a positive impact on the chemical industry by providing safer, more efficient chemical manufacturing processes that have reduced the use of toxic chemicals, harsh reaction conditions, and expensive metal catalysts, which has improved alignment with the principles of Green Chemistry. The genetically-modified (GM) biocatalysts that are utilized in these processes are typically separated from high-value products and then recycled, or eliminated. Elimination routes include disposal in sanitary landfills, incineration, use as a fuel, animal feed, or reuse as an agricultural soil amendment or other value-added products. Elimination routes that have the potential to impact the food chain or environment have been more heavily scrutinized for the fate and persistence of biological products. In this study, we developed and optimized a method for monitoring the degradation of strain-specific DNA markers from a genetically-modified organism (GMO) used for the commercial production of 1,3-propanediol. Laboratory and field tests showed that a marker for heterologous DNA in the GM organism was no longer detectable by end-point polymerase chain reaction (PCR) after 14 days. The half-life of heterologous DNA was increased by 17% (from 42.4 to 49.7 h) after sterilization of the soil from a field plot, which indicated that abiotic factors were important in degradation of DNA under field conditions. There was no evidence for horizontal transfer of DNA target sequences from the GMO to viable organisms present in the soil.

  2. Lactoferrin Directly Scavenges Hydroxyl Radicals and Undergoes Oxidative Self-Degradation: A Possible Role in Protection against Oxidative DNA Damage

    Directory of Open Access Journals (Sweden)

    Yuki Ogasawara


    Full Text Available In this study, we examined the protective effect of lactoferrin against DNA damage induced by various hydroxyl radical generation systems. Lactoferrin (LF was examined with regard to its potential role as a scavenger against radical oxygen species using bovine milk LF. Native LF, iron-saturated LF (holo-LF, and apolactoferrin (apo-LF effectively suppressed strand breaks in plasmid DNA due to hydroxyl radicals produced by the Fenton reaction. In addition, both native LF and holo-LF clearly protected calf thymus DNA from fragmentation due to ultraviolet irradiation in the presence of H2O2. We also demonstrated a protective effect of all three LF molecules against 8-hydroxydeoxyguanosine (8-OHdG formation in calf thymus DNA following ultraviolet (UV irradiation with H2O2. Our results clearly indicate that native LF has reactive oxygen species-scavenging ability, independent of its nature as a masking component for transient metals. We also demonstrated that the protective effect of LF against oxidative DNA damage is due to degradation of LF itself, which is more susceptible to degradation than other bovine milk proteins.

  3. Combined treatment with vitamin B12b and ascorbic acid causes in vitro DNA degradation in tumor cells. (United States)

    Medvedev, A I; Akatov, V S; Kreshchenko, N D; Solov'eva, M E; Leshchenko, V V; Lezhnev, E I; Yakubovskaya, R I


    Incubation of Ehrlich ascites carcinoma and HEp-2 human epidermoid laryngeal carcinoma cells with hydroxycobalamin (vitamin B12b) and ascorbic acid induced generation and accumulation of double-stranded DNA fragments (23,000 b.p. and longer) in cells. The same vitamins alone in the same concentrations produced no such effects. DNA degradation in HEp-2 cells caused by long-term (4 h) incubation with 5-25 microM hydroxycobalamin and ascorbic acid (1:10-1:40 molar ratio) at 37 degrees C was comparable with that induced by gamma-irradiation in a dose of 150 Gy at 4 degrees C.

  4. Degradation of 4-nitrophenol (4-NP) using ZnO nanoparticles supported on zeolites and modeling of experimental results by artificial neural networks

    Energy Technology Data Exchange (ETDEWEB)

    Khatamian, Masumeh, E-mail: [Inorganic Chemistry Department, Faculty of Chemistry, University of Tabriz, C.P. 51664 Tabriz (Iran, Islamic Republic of); Divband, Baharak [Inorganic Chemistry Department, Faculty of Chemistry, University of Tabriz, C.P. 51664 Tabriz (Iran, Islamic Republic of); Jodaei, Azadeh [Applied Chemistry, Islamic Azad University, Sofian Branch, Sofian (Iran, Islamic Republic of)


    Graphical abstract: ZnO/Zeolites (HY, HZSM-5, and Clinoptilolite) nanocomposites are prepared by using poly acrylamide pyrolysis method for the first time. Among the catalysts, ZnO/HZSM-5 was the best in photocatalytic degradation of 4-nitrophenol and the time required for complete mineralization under ambient visible light was 75 min. These results are in good agreement with predicted results of the designed artificial neural networks (ANNs) model. Highlights: Black-Right-Pointing-Pointer ZnO/Zeolites (HY, HZSM-5, Clinoptiolite) are used for degradation of 4-nitrophenol. Black-Right-Pointing-Pointer ZnO/Zeolites nanocomposites are prepared by using poly acrylamide pyrolysis method. Black-Right-Pointing-Pointer Among the catalysts, ZnO/HZSM-5 showed higher percentage of adsorption than others. Black-Right-Pointing-Pointer Predicted results of the designed ANN model and experimental data are in good agreements. - Abstract: In this paper, we report the synthesis of ZnO, ZnO/HZSM-5, ZnO/HY and ZnO/Clin by a poly acrylamide pyrolysis method for the first time. The presences of carbon network/cages in the poly acrylamide gel can effectively prevent particle agglomeration. The catalytic activity of all specimens was tested by carrying out the 4-nitrophenol degradation, used as a 'probe' reaction, in the aqueous medium under ambient visible light. The prepared samples were characterized by X-ray diffraction (XRD), specific surface area (BET) and porosity determination, scanning electron microscopy (SEM) coupled with energy dispersive X-ray analysis (EDX), visible-ultraviolet diffuse reflectance spectroscopy (DRS) and Fourier transform infrared spectroscopy (FT-IR), to evaluate particle structure, size distribution and composition. The results revealed that among the catalysts, ZnO/HZSM-5 showed higher percentage of adsorption than others. The time required for complete mineralization of 4-NP under ambient visible light over ZnO/HZSM-5 was 75 min. The higher

  5. Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples

    DEFF Research Database (Denmark)

    Børsting, Claus; Mogensen, Helle Smidt; Morling, Niels


    Heterozygote imbalances leading to allele drop-outs and disproportionally large stutters leading to allele drop-ins are known stochastic phenomena related to STR typing of low-template DNA (LtDNA). The large stutters and the many drop-ins in typical STR stutter positions are artifacts from the PCR...

  6. Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples

    DEFF Research Database (Denmark)

    Børsting, Claus; Mogensen, Helle Smidt; Morling, Niels


    Heterozygote imbalances leading to allele drop-outs and disproportionally large stutters leading to allele drop-ins are known stochastic phenomena related to STR typing of low-template DNA (LtDNA). The large stutters and the many drop-ins in typical STR stutter positions are artifacts from the PCR...

  7. Proteasomal degradation of herpes simplex virus capsids in macrophages releases DNA to the cytosol for recognition by DNA sensors

    NARCIS (Netherlands)

    Horan, K.A.; Hansen, K.; Jakobsen, M.R.; Holm, C.K.; Soby, S.; Unterholzner, L.; Thompson, M.; West, J.A.; Iversen, M.B.; Rasmussen, S.B.; Ellermann-Eriksen, S.; Kurt-Jones, E.; Landolfo, S.; Damania, B.; Melchjorsen, J.; Bowie, A.G.; Fitzgerald, K.A.; Paludan, S.R.


    The innate immune system is important for control of infections, including herpesvirus infections. Intracellular DNA potently stimulates antiviral IFN responses. It is known that plasmacytoid dendritic cells sense herpesvirus DNA in endosomes via TLR9 and that nonimmune tissue cells can sense herpes

  8. Evaluation of PCR, DNA hybridization and immunomagnetic separation - PCR for detection of Burkholderia mallei in artificially inoculated environmental samples. (United States)

    Merwyn, S; Kumar, S; Agarwal, G S; Rai, G P


    Glanders is highly contagious disease of equines, caused by Burkholderia mallei. The disease though rare, can be transmitted to humans. Here, we report a strategy for rapid detection of B. mallei from environmental samples. Different bacteriological media were evaluated and brain heart infusion broth medium with selective supplements (BHIB-SS) of penicillin (200 U/ml) and crystal violet (1:10,00000) was found to support the maximum growth of B. mallei even in the presence of other bacteria like Escherichia coli and Staphylococcus aureus. A polymerase chain reaction (PCR) and a DNA hybridization method was standardized for 823 bp specific dNA sequence of B. mallei. To enable the quicker and direct enrichment of B. mallei bacteria from environmental samples, an immunomagnetic separation (IMS) method was also standardized. Water, husk, grass and gram samples were artificially contaminated by B. mallei bacteria and after enrichment of B. mallei in BHIB-SS, detection was carried out by PCR and DNA hybridization. PCR was found to be a better method of the two with a detection limit of 10(4)-10(6) CFU/ml (6 h enrichment in BHIB-SS) in water and other particulate matrices. Detection by PCR in the above samples without enrichment in BHIBSS was carried out following IMS where the detection limit was about 1-2 log higher than PCR following enrichment in BHIB-SS. We recommend PCR for 823 bp for detection of B. mallei from environmental samples either following enrichment in BHIB-SS or IMS. IMS-PCR method may be preferred in situations where numbers of B. mallei bacteria are expected to be high and results are required in short time.

  9. Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn. (United States)

    Woodruff, S P; Johnson, T R; Waits, L P


    Knowledge of population demographics is important for species management but can be challenging in low-density, wide-ranging species. Population monitoring of the endangered Sonoran pronghorn (Antilocapra americana sonoriensis) is critical for assessing the success of recovery efforts, and noninvasive DNA sampling (NDS) could be more cost-effective and less intrusive than traditional methods. We evaluated faecal pellet deposition rates and faecal DNA degradation rates to maximize sampling efficiency for DNA-based mark-recapture analyses. Deposition data were collected at five watering holes using sampling intervals of 1-7 days and averaged one pellet pile per pronghorn per day. To evaluate nuclear DNA (nDNA) degradation, 20 faecal samples were exposed to local environmental conditions and sampled at eight time points from one to 124 days. Average amplification success rates for six nDNA microsatellite loci were 81% for samples on day one, 63% by day seven, 2% by day 14 and 0% by day 60. We evaluated the efficiency of different sampling intervals (1-10 days) by estimating the number of successful samples, success rate of individual identification and laboratory costs per successful sample. Cost per successful sample increased and success and efficiency declined as the sampling interval increased. Results indicate NDS of faecal pellets is a feasible method for individual identification, population estimation and demographic monitoring of Sonoran pronghorn. We recommend collecting samples sampling interval of four to seven days in summer conditions (i.e., extreme heat and exposure to UV light) will achieve desired sample sizes for mark-recapture analysis while also maximizing efficiency [Corrected]. © 2014 John Wiley & Sons Ltd.


    Directory of Open Access Journals (Sweden)



    Full Text Available A heterogeneous photo-Fenton-like degradation process of 1-naphthol (1-NP promoted by natural iron oxide (NIO in the presence of H2O2 was studied under artificial (365 nm and solar irradiation. This is an important reaction for the environment since both H2O2 and iron oxides are common constituents of natural waters. Furthermore, iron oxides function as catalysts in chemical oxidation processes used with H2O2 for treatment of contaminated waters. The NIO used in this study was characterized by X-ray diffraction (XRD, X-ray fluorescence and Brunauer–Emmett–Teller (BET methods. The results show that the NIO is a composite material that contains predominantly crystalline hematite particales (Fe2O3. The Fe2O3 in NIO was able to initiate the Fenton-like and photo-Fenton-like reactions. The effects of initial pH, catalyst dosage, H2O2 concentration and the wavelength of the light source (UV and solar on the photodegradation of 1-NP were investigated. The optimal content of the NIO was 1 g L-1 and the optimal H2O2 concentration was 10 mM. The degradation could occur efficiently over a wide pH range of 3-8.3. Furthermore, an important effect of light was observed. The photo-oxidation of 1-NP in NIO-H2O2 system under solar light was significantly accelerated in comparison with artificial irradiation at 365 nm.

  11. Prediction of HPLC retention times of tebipenem pivoxyl and its degradation products in solid state by applying adaptive artificial neural network with recursive features elimination. (United States)

    Mizera, Mikołaj; Talaczyńska, Alicja; Zalewski, Przemysław; Skibiński, Robert; Cielecka-Piontek, Judyta


    A sensitive and fast HPLC method using ultraviolet diode-array detector (DAD)/electrospray ionization tandem mass spectrometry (Q-TOF-MS/MS) was developed for the determination of tebipenem pivoxyl and in the presence of degradation products formed during thermolysis. The chromatographic separations were performed on stationary phases produced in core-shell technology with particle diameter of 5.0 µm. The mobile phases consisted of formic acid (0.1%) and acetonitrile at different ratios. The flow rate was 0.8 mL/min while the wavelength was set at 331 nm. The stability characteristics of tebipenem pivoxyl were studied by performing stress tests in the solid state in dry air (RH=0%) and at an increased relative air humidity (RH=90%). The validation parameters such as selectivity, accuracy, precision and sensitivity were found to be satisfying. The satisfied selectivity and precision of determination were obtained for the separation of tebipenem pivoxyl from its degradation products using a stationary phase with 5.0 µm particles. The evaluation of the chemical structure of the 9 degradation products of tebipenem pivoxyl was conducted following separation based on the stationary phase with a 5.0 µm particle size by applying a Q-TOF-MS/MS detector. The main degradation products of tebipenem pivoxyl were identified: a product resulting from the condensation of the substituents of 1-(4,5-dihydro-1,3-thiazol-2-yl)-3-azetidinyl]sulfanyl and acid and ester forms of tebipenem with an open β-lactam ring in dry air at an increased temperature (RH=0%, T=393 K) as well as acid and ester forms of tebipenem with an open β-lactam ring at an increased relative air humidity and an elevated temperature (RH=90%, T=333 K). Retention times of tebipenem pivoxyl and its degradation products were used as training data set for predictive model of quantitative structure-retention relationship. An artificial neural network with adaptation protocol and extensive feature selection process

  12. Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

    Energy Technology Data Exchange (ETDEWEB)

    Song, Mengke [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Jiang, Longfei [College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 (China); Zhang, Dayi [Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ (United Kingdom); Luo, Chunling, E-mail: [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Wang, Yan [Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024 (China); Yu, Zhiqiang [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Yin, Hua [College of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); Zhang, Gan [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China)


    Highlights: • Investigate PAHs degraders in forest carbon-rich soils via DNA-SIP. • Rhodanobacter is identified to metabolite anthracene for the first time. • The first fluoranthene degrader belongs to Acidobacteria. • Different functions of PAHs degraders in forest soils from contaminated soils. - Abstract: Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually {sup 13}C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

  13. Nuclear translocation of p21{sup WAF1/CIP1} protein prior to its cytosolic degradation by UV enhances DNA repair and survival

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ji Young; Kim, Hee Suk; Kim, Joo Young [Department of Biochemistry, Korea University College of Medicine, Seoul 136-705 (Korea, Republic of); Sohn, Jeongwon, E-mail: [Department of Biochemistry, Korea University College of Medicine, Seoul 136-705 (Korea, Republic of)


    We previously reported that UV induced rapid proteasomal degradation of p21 protein in an ubiquitination-independent manner. Here, UV-induced p21 proteolysis was found to occur in the cytosol. Before cytosolic degradation, however, p21 protein translocated to and transiently accumulated in the nucleus. Nuclear translocation of p21 was not required for its degradation, but rather promoted DNA repair and cell survival. Overexpression of the wild type p21, but not the one with defective nuclear localization signal (NLS), reduced UV-induced DNA damage and cell death. Some of p21 protein translocated to the nucleus were associated with chromatin-bound PCNA and saved from UV-induced proteolysis. These data together show that p21 translocates to the nucleus to participate in DNA repair, while the rest is rapidly degraded in the cytosol. We propose that our findings reflect a mechanism to facilitate removal of damaged cells, enhancing DNA repair at the same time.

  14. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology (United States)

    Koizumi, Yoshikazu; Kelly, John J.; Nakagawa, Tatsunori; Urakawa, Hidetoshi; El-Fantroussi, Said; Al-Muzaini, Saleh; Fukui, Manabu; Urushigawa, Yoshikuni; Stahl, David A.


    A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific for the 16S rRNAs of target organisms corresponding to T-1, E-1, and E-2 were designed, and hybridization conditions were optimized for two analytical formats, membrane and DNA microarray hybridization. Both formats were used to characterize the TDC and EDC, and the results of both were consistent with DGGE analysis. In order to assess the utility of the microarray format for analysis of environmental samples, oil-contaminated sediments from the coast of Kuwait were analyzed. The DNA microarray successfully detected bacterial nucleic acids from these samples, but probes targeting specific groups of sulfate-reducing bacteria did not give positive signals. The results of this study demonstrate the limitations and the potential utility of DNA microarrays for microbial community analysis.

  15. An easy and versatile 2-step protocol for targeted modification and subcloning of DNA from bacterial artificial chromosomes using non-commercial plasmids

    Directory of Open Access Journals (Sweden)

    Hartwich Heiner


    Full Text Available Abstract Background Promoter-specific expression of foreign DNA in transgenic organisms often relies on bacterial artificial chromosomes (BACs. This approach requires modification and subcloning of BAC-DNA by recombineering technologies in Escherichia coli. Most current protocols rely on commercial kits or isolation of BACs, their transfer between different host strains, and their restriction. Findings In this report we present a 2-step protocol for efficient modification and subcloning of DNA from bacterial artificial chromosomes using the non-commercial plasmids pKM208 and pTP223, distributed from A targeting cassette was successfully integrated into a BAC and 42 kb of this construct were subcloned. Both a plasmid-derived substrate with longer homology arms and a PCR-generated substrate with short homology arms (50 bp were used for recombination. pKM208 and pTP223 contain all required genes for recombineering, but differ in their antibiotic resistance genes. This makes the system independent of the selection markers on the DNA molecules targeted for recombination. Conclusions The time and cost saving protocol presented here compares favorably to currently used systems. Using non-commercial plasmids, it allows targeted modification and cloning of large DNA (> 40 kb fragments in vivo without restriction and ligation. Furthermore, both steps are performed in the same host eliminating the need to isolate BAC DNA and to use different bacterial strains.

  16. Is passive transmission of non-viral vectors through artificial insemination of sperm-DNA mixtures sufficient for chicken transgenesis? (United States)

    Chaparian, Shahram; Abdulahnejad, Ahad; Rashidi, Farzad; Toghyani, Majid; Gheisari, Abbasali; Eghbalsaied, Shahin


    DNA uptake in the post-acrosomal region of the spermatozoa takes place exclusively in immotile spermatozoa that are naturally unable to fertilize eggs. The present study aimed to assess whether passive transmission of non-viral vectors to the surrounding areas of chicken embryos could be an alternate mechanism in chicken sperm-mediated gene transfer. First, the presence of nucleases in rooster seminal plasma was evaluated. Semen ejaculates from five roosters were centrifuged and the supernatant was incubated with pBL2 for 1 h. A robust nuclease cocktail was detected in the rooster semen. To overcome these nucleases, plasmid-TransIT combinations were incubated with semen for 1 h. Incubation of exogenous DNA in the lipoplex structure could considerably bypass the semen nuclease effect. Then, intravaginal insemination of 1 × 10(9) sperm mixed with lipoplexes (40 µg pBL2:40 µl TransIT) was carried out in 15 virgin hens. Neither the epithelial tissue from the inseminated female reproductive tracts nor the produced embryos following artificial insemination showed the transgene. To remove any bias in the transgene transmission possibility, the plasmid-TransIT admixture was directly injected in close vicinity of the embryos in newly laid eggs. Nonetheless, none of the produced fetuses or chicks carried the transgene. In conclusion, the results of the present study revealed a nuclease admixture in rooster seminal plasma, and passive/active transmission of the non-viral vector into close vicinity of the chicken embryo was inefficient for producing transgenic chicks.

  17. 16S ribosomal DNA clone libraries to reveal bacterial diversity in anaerobic reactor-degraded tetrabromobisphenol A. (United States)

    Peng, Xingxing; Zhang, Zaili; Zhao, Ziling; Jia, Xiaoshan


    Microorganisms able to rapidly degrade tetrabromobisphenol A (TBBPA) were domesticated in an anaerobic reactor and added to gradually increased concentrations of TBBPA. After 240 days of domestication, the degradation rate reached 96.0% in cultivated batch experiments lasting 20 days. The optimum cultivating temperature and pH were 30°C and 7.0. The bacterial community's composition and diversity in the reactor was studied by comparative analysis with 16S ribosomal DNA clone libraries. Amplified rDNA restriction analysis of 200 clones from the library indicate that the rDNA richness was high (Coverage C 99.5%) and that evenness was not high (Shannon-Weaver index 2.42). Phylogenetic analysis of 63 bacterial sequences from the reactor libraries demonstrated the presence of Betaproteobacteria (33.1%), Gammaproteobacteria (18.7%), Bacteroidetes (13.9%), Firmicutes (11.4%), Chloroflexi (3.6%), Actinobacteria (0.6%), the candidate division TM7 (4.2%) and other unknown, uncultured bacterial groups (14.5%). Comamonas, Achromobacter, Pseudomonas and Flavobacterium were the dominant types.

  18. Rad51 recombinase prevents Mre11 nuclease-dependent degradation and excessive PrimPol-mediated elongation of nascent DNA after UV irradiation. (United States)

    Vallerga, María Belén; Mansilla, Sabrina F; Federico, María Belén; Bertolin, Agustina P; Gottifredi, Vanesa


    After UV irradiation, DNA polymerases specialized in translesion DNA synthesis (TLS) aid DNA replication. However, it is unclear whether other mechanisms also facilitate the elongation of UV-damaged DNA. We wondered if Rad51 recombinase (Rad51), a factor that escorts replication forks, aids replication across UV lesions. We found that depletion of Rad51 impairs S-phase progression and increases cell death after UV irradiation. Interestingly, Rad51 and the TLS polymerase polη modulate the elongation of nascent DNA in different ways, suggesting that DNA elongation after UV irradiation does not exclusively rely on TLS events. In particular, Rad51 protects the DNA synthesized immediately before UV irradiation from degradation and avoids excessive elongation of nascent DNA after UV irradiation. In Rad51-depleted samples, the degradation of DNA was limited to the first minutes after UV irradiation and required the exonuclease activity of the double strand break repair nuclease (Mre11). The persistent dysregulation of nascent DNA elongation after Rad51 knockdown required Mre11, but not its exonuclease activity, and PrimPol, a DNA polymerase with primase activity. By showing a crucial contribution of Rad51 to the synthesis of nascent DNA, our results reveal an unanticipated complexity in the regulation of DNA elongation across UV-damaged templates.

  19. DNA methylation-based forensic age prediction using artificial neural networks and next generation sequencing. (United States)

    Vidaki, Athina; Ballard, David; Aliferi, Anastasia; Miller, Thomas H; Barron, Leon P; Syndercombe Court, Denise


    The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging can be complex and is associated with various molecular modifications in cells that accumulate over a person's lifetime including epigenetic patterns. The aim of this study was to use age-specific DNA methylation patterns to generate an accurate model for the prediction of chronological age using data from whole blood. In total, 45 age-associated CpG sites were selected based on their reported age coefficients in a previous extensive study and investigated using publicly available methylation data obtained from 1156 whole blood samples (aged 2-90 years) analysed with Illumina's genome-wide methylation platforms (27K/450K). Applying stepwise regression for variable selection, 23 of these CpG sites were identified that could significantly contribute to age prediction modelling and multiple regression analysis carried out with these markers provided an accurate prediction of age (R(2)=0.92, mean absolute error (MAE)=4.6 years). However, applying machine learning, and more specifically a generalised regression neural network model, the age prediction significantly improved (R(2)=0.96) with a MAE=3.3 years for the training set and 4.4 years for a blind test set of 231 cases. The machine learning approach used 16 CpG sites, located in 16 different genomic regions, with the top 3 predictors of age belonged to the genes NHLRC1, SCGN and CSNK1D. The proposed model was further tested using independent cohorts of 53 monozygotic twins (MAE=7.1 years) and a cohort of 1011 disease state individuals (MAE=7.2 years). Furthermore, we highlighted the age markers' potential applicability in samples other than blood by predicting age with similar accuracy in 265 saliva samples (R(2)=0.96) with a MAE=3.2 years (training set) and 4.0 years (blind test). In an attempt to create a sensitive and accurate age prediction test, a next

  20. Natural versus artificial creation of base pairs in DNA: origin of nucleobases from the perspectives of unnatural base pair studies. (United States)

    Hirao, Ichiro; Kimoto, Michiko; Yamashige, Rie


    Since life began on Earth, the four types of bases (A, G, C, and T(U)) that form two sets of base pairs have remained unchanged as the components of nucleic acids that replicate and transfer genetic information. Throughout evolution, except for the U to T modification, the four base structures have not changed. This constancy within the genetic code raises the question of how these complicated nucleotides were generated from the molecules in a primordial soup on the early Earth. At some prebiotic stage, the complementarity of base pairs might have accelerated the generation and accumulation of nucleotides or oligonucleotides. We have no clues whether one pair of nucleobases initially appeared on the early Earth during this process or a set of two base pairs appeared simultaneously. Recently, researchers have developed new artificial pairs of nucleobases (unnatural base pairs) that function alongside the natural base pairs. Some unnatural base pairs in duplex DNA can be efficiently and faithfully amplified in a polymerase chain reaction (PCR) using thermostable DNA polymerases. The addition of unnatural base pair systems could expand the genetic alphabet of DNA, thus providing a new mechanism for the generation novel biopolymers by the site-specific incorporation of functional components into nucleic acids and proteins. Furthermore, the process of unnatural base pair development might provide clues to the origin of the natural base pairs in a primordial soup on the early Earth. In this Account, we describe the development of three representative types of unnatural base pairs that function as a third pair of nucleobases in PCR and reconsider the origin of the natural nucleic acids. As researchers developing unnatural base pairs, they use repeated "proof of concept" experiments. As researchers design new base pairs, they improve the structures that function in PCR and eliminate those that do not. We expect that this process is similar to the one functioning in the

  1. Sliding Window Analyses for Optimal Selection of Mini-Barcodes, and Application to 454-Pyrosequencing for Specimen Identification from Degraded DNA

    DEFF Research Database (Denmark)

    Boyer, Stephane; Brown, Samuel D J; Collins, Rupert A


    DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI) is over 600 base pairs (bp), amplifi......DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI) is over 600 base pairs (bp...... primers were designed and used to amplify degraded earthworm (prey) DNA from 46 landsnail (predator) faeces using 454-pyrosequencing. This led to the detection of 18 earthworm species in the diet of the snail. We encourage molecular ecologists to use this method to objectively select the most informative...

  2. Distortion of genetically modified organism quantification in processed foods: influence of particle size compositions and heat-induced DNA degradation. (United States)

    Moreano, Francisco; Busch, Ulrich; Engel, Karl-Heinz


    Milling fractions from conventional and transgenic corn were prepared at laboratory scale and used to study the influence of sample composition and heat-induced DNA degradation on the relative quantification of genetically modified organisms (GMO) in food products. Particle size distributions of the obtained fractions (coarse grits, regular grits, meal, and flour) were characterized using a laser diffraction system. The application of two DNA isolation protocols revealed a strong correlation between the degree of comminution of the milling fractions and the DNA yield in the extracts. Mixtures of milling fractions from conventional and transgenic material (1%) were prepared and analyzed via real-time polymerase chain reaction. Accurate quantification of the adjusted GMO content was only possible in mixtures containing conventional and transgenic material in the form of analogous milling fractions, whereas mixtures of fractions exhibiting different particle size distributions delivered significantly over- and underestimated GMO contents depending on their compositions. The process of heat-induced nucleic acid degradation was followed by applying two established quantitative assays showing differences between the lengths of the recombinant and reference target sequences (A, deltal(A) = -25 bp; B, deltal(B) = +16 bp; values related to the amplicon length of the reference gene). Data obtained by the application of method A resulted in underestimated recoveries of GMO contents in the samples of heat-treated products, reflecting the favored degradation of the longer target sequence used for the detection of the transgene. In contrast, data yielded by the application of method B resulted in increasingly overestimated recoveries of GMO contents. The results show how commonly used food technological processes may lead to distortions in the results of quantitative GMO analyses.

  3. Altering an Artificial Gagpolnef Polyprotein and Mode of ENV Co-Administration Affects the Immunogenicity of a Clade C HIV DNA Vaccine


    Katharina Böckl; Jens Wild; Simon Bredl; Kathrin Kindsmüller; Josef Köstler; Ralf Wagner


    HIV-1 candidate vaccines expressing an artificial polyprotein comprising Gag, Pol and Nef (GPN) and a secreted envelope protein (Env) were shown in recent Phase I/II clinical trials to induce high levels of polyfunctional T cell responses; however, Env-specific responses clearly exceeded those against Gag. Here, we assess the impact of the GPN immunogen design and variations in the formulation and vaccination regimen of a combined GPN/Env DNA vaccine on the T cell responses against the variou...

  4. Identification of a Toluene-Degrading Bacterium from a Soil Sample through H218O DNA Stable Isotope Probing ▿† (United States)

    Woods, Angela; Watwood, Maribeth; Schwartz, Egbert


    DNA stable isotope probing (DNA-SIP) with H218O was used to identify a toluene-degrading bacterium in soil amended with 48 ppm toluene. After quantification of toluene degradation rates in soil, DNA was extracted from soil incubated with H218O, H216O, H216O and 48 ppm toluene, or H218O and 48 ppm toluene. A single DNA band formed along a cesium chloride gradient after isopycnic centrifugation of extracts from soils incubated with H216O. With extracts from soils to which only H218O was added, two distinct DNA bands formed, while three bands formed when DNA extracted from soil incubated with both H218O and toluene was analyzed. We suggest that this third band formed because toluene does not contain any oxygen atoms and toluene-degrading organisms had to transfer oxygen atoms from H218O into metabolic intermediates to form nucleic acids de novo. We extracted the third DNA band and amplified a large fraction of the bacterial 16S rRNA gene. Direct sequencing of the PCR product obtained from the labeled DNA, as well as cloned 16S rRNA amplicons, identified a known toluene degrader, Rhodococcus jostii RHA1. A toluene-degrading bacterial strain was subsequently isolated from soil and shown to be Rhodococcus jostii RHA1. Finally, quantitative real-time PCR analysis showed that the abundance of the 16S rRNA gene of Rhodococcus jostii RHA1 increased in soil after toluene exposure but not in soils from which toluene was withheld. This study indicates that H218O DNA-SIP can be a useful method for identifying pollutant-degrading bacteria in soil. PMID:21742928

  5. Correlative Analysis on the Relationship between PMI and DNA Degradation of Cell Nucleus in Human Different Tissues

    Institute of Scientific and Technical Information of China (English)

    SHU Xiji; LIU Yaling; REN Liang; HE Fanggang; ZHOU Hongyan; LIU Lijiang; LIU Liang


    To determining the postmortem interval (PMI) through quantitative analysis of the DNA degradation of cell nucleus in human brain and spleen by using image analysis technique (IAT). The brain and spleen tissues from 32 cadavers with known PMI were collected, subjected to cell smear every 1 h within the first 5-36 h after death, stained by Feulgen-Van's staining, Three indices reflecting DNA in brain cells (astrocytes) and splenic lymphocytes, including integral optical density (IOD), average optical density (AOD), average gray (AG) were measured by employing the mage analysis instrument. The results showed that IOD and AOD declined and AG increased with the prolongation of dead time within 5-36 h. A correlation between the PMI and gray parameters (IOD,AOD and AG) was identified and the corresponding regression equation was obtained. The parameters (IOD,AOD and AG) were proved to be effective quantitative indicators for accurate estimation of PMI within 5-36 h after death.

  6. Correlative analysis on the relationship between PMI and DNA degradation of cell nucleus in human different tissues. (United States)

    Shu, Xiji; Liu, Yaling; Ren, Liang; He, Fanggang; Zhou, Hongyan; Liu, Lijiang; Liu, Liang


    To determining the postmortem interval (PMI) through quantitative analysis of the DNA degradation of cell nucleus in human brain and spleen by using image analysis technique (IAT). The brain and spleen tissues from 32 cadavers with known PMI were collected, subjected to cell smear every 1 h within the first 5-36 h after death, stained by Feulgen-Van's staining, Three indices reflecting DNA in brain cells (astrocytes) and splenic lymphocytes, including integral optical density (IOD), average optical density (AOD), average gray (AG) were measured by employing the mage analysis instrument. The results showed that IOD and AOD declined and AG increased with the prolongation of dead time within 5-36 h. A correlation between the PMI and gray parameters (IOD, AOD and AG) was identified and the corresponding regression equation was obtained. The parameters (IOD, AOD and AG) were proved to be effective quantitative indicators for accurate estimation of PMI within 5-36 h after death.

  7. Sliding window analyses for optimal selection of mini-barcodes, and application to 454-pyrosequencing for specimen identification from degraded DNA.

    Directory of Open Access Journals (Sweden)

    Stephane Boyer

    Full Text Available DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI is over 600 base pairs (bp, amplification fails when the DNA molecule is degraded into smaller fragments. However, relevant information for specimen identification may not be evenly distributed along the barcoding region, and a shorter target can be sufficient for identification purposes. This study proposes a new, widely applicable, method to compare the performance of all potential 'mini-barcodes' for a given molecular marker and to objectively select the shortest and most informative one. Our method is based on a sliding window analysis implemented in the new R package SPIDER (Species IDentity and Evolution in R. This method is applicable to any taxon and any molecular marker. Here, it was tested on earthworm DNA that had been degraded through digestion by carnivorous landsnails. A 100 bp region of 16 S rDNA was selected as the shortest informative fragment (mini-barcode required for accurate specimen identification. Corresponding primers were designed and used to amplify degraded earthworm (prey DNA from 46 landsnail (predator faeces using 454-pyrosequencing. This led to the detection of 18 earthworm species in the diet of the snail. We encourage molecular ecologists to use this method to objectively select the most informative region of the gene they aim to amplify from degraded DNA. The method and tools provided here, can be particularly useful (1 when dealing with degraded DNA for which only small fragments can be amplified, (2 for cases where no consensus has yet been reached on the appropriate barcode gene, or (3 to allow direct analysis of short reads derived from massively parallel sequencing without the need for bioinformatic consolidation.

  8. Purification of Single-Stranded cDNA Based on RNA Degradation Treatment and Adsorption Chromatography. (United States)

    Trujillo-Esquivel, Elías; Franco, Bernardo; Flores-Martínez, Alberto; Ponce-Noyola, Patricia; Mora-Montes, Héctor M


    Analysis of gene expression is a common research tool to study networks controlling gene expression, the role of genes with unknown function, and environmentally induced responses of organisms. Most of the analytical tools used to analyze gene expression rely on accurate cDNA synthesis and quantification to obtain reproducible and quantifiable results. Thus far, most commercial kits for isolation and purification of cDNA target double-stranded molecules, which do not accurately represent the abundance of transcripts. In the present report, we provide a simple and fast method to purify single-stranded cDNA, exhibiting high purity and yield. This method is based on the treatment with RNase H and RNase A after cDNA synthesis, followed by separation in silica spin-columns and ethanol precipitation. In addition, our method avoids the use of DNase I to eliminate genomic DNA from RNA preparations, which improves cDNA yield. As a case report, our method proved to be useful in the purification of single-stranded cDNA from the pathogenic fungus Sporothrix schenckii.

  9. Phosphorylation of Hdmx mediates its Hdm2- and ATM-dependent degradation in response to DNA damage. (United States)

    Pereg, Yaron; Shkedy, Dganit; de Graaf, Petra; Meulmeester, Erik; Edelson-Averbukh, Marina; Salek, Mogjiborahman; Biton, Sharon; Teunisse, Amina F A S; Lehmann, Wolf D; Jochemsen, Aart G; Shiloh, Yosef


    Maintenance of genomic stability depends on the DNA damage response, an extensive signaling network that is activated by DNA lesions such as double-strand breaks (DSBs). The primary activator of the mammalian DSB response is the nuclear protein kinase ataxia-telangiectasia, mutated (ATM), which phosphorylates key players in various arms of this network. The activation and stabilization of the p53 protein play a major role in the DNA damage response and are mediated by ATM-dependent posttranslational modifications of p53 and Mdm2, a ubiquitin ligase of p53. p53's response to DNA damage also depends on Mdm2-dependent proteolysis of Mdmx, a homologue of Mdm2 that represses p53's transactivation function. Here we show that efficient damage-induced degradation of human Hdmx depends on functional ATM and at least three sites on the Hdmx that are phosphorylated in response to DSBs. One of these sites, S403, is a direct ATM target. Accordingly, each of these sites is important for Hdm2-mediated ubiquitination of Hdmx after DSB induction. These results demonstrate a sophisticated mechanism whereby ATM fine-tunes the optimal activation of p53 by simultaneously modifying each player in the process.

  10. OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands

    Directory of Open Access Journals (Sweden)

    Kevin M. Bradley


    Full Text Available Synthetic biologists wishing to self-assemble large DNA (L-DNA constructs from small DNA fragments made by automated synthesis need fragments that hybridize predictably. Such predictability is difficult to obtain with nucleotides built from just the four standard nucleotides. Natural DNA's peculiar combination of strong and weak G:C and A:T pairs, the context-dependence of the strengths of those pairs, unimolecular strand folding that competes with desired interstrand hybridization, and non-Watson–Crick interactions available to standard DNA, all contribute to this unpredictability. In principle, adding extra nucleotides to the genetic alphabet can improve the predictability and reliability of autonomous DNA self-assembly, simply by increasing the information density of oligonucleotide sequences. These extra nucleotides are now available as parts of artificially expanded genetic information systems (AEGIS, and tools are now available to generate entirely standard DNA from AEGIS DNA during PCR amplification. Here, we describe the OligArch (for "oligonucleotide architecting" software, an application that permits synthetic biologists to engineer optimally self-assembling DNA constructs from both six- and eight-letter AEGIS alphabets. This software has been used to design oligonucleotides that self-assemble to form complete genes from 20 or more single-stranded synthetic oligonucleotides. OligArch is therefore a key element of a scalable and integrated infrastructure for the rapid and designed engineering of biology.

  11. Evaluation of a commercial in-clinic point-of-care polymerase chain reaction test for Ehrlichia canis DNA in artificially infected dogs. (United States)

    Waner, Trevor; Nachum-Biala, Yaarit; Harrus, Shimon


    A novel in-clinic point-of-care (ICPOC) polymerase chain reaction (PCR) test was evaluated for its ability to detect Ehrlichia canis DNA in artificially infected dogs compared to a real-time PCR assay. Six Beagle dogs negative for E. canis antibodies and PCR negative were artificially infected with an Israeli E. canis strain (611). All dogs developed IgG antibodies 8 days post infection (PI), and clinical and hematological abnormalities on day 10 PI. Only the real-time PCR detected E. canis DNA in the blood of five dogs at days 3 and 5 PI. At day 12 PI during the acute phase of the disease, 1 day after the initiation of doxycycline treatment, the ICPOC PCR assay detected E. canis DNA in all infected dogs, which were also positive by the real-time PCR. Two days later the ICPOC PCR assay was able to detect only 3/6 infected dogs, which were all positive by the real-time PCR. At days 17 and 19 PI, the ICPOC PCR assay did not detect E. canis DNA in the dogs while the real-time PCR detected all dogs as positive on day 17 PI and two dogs on day 19 PI. In conclusion, the sensitivity of the ICPOC PCR assay was 75% for the acute phase of the disease and 30% for the whole study, suggesting that this ICPOC assay has a potential utility for the diagnosis of acute canine monocytic ehrlichiosis.

  12. Degradation of mitochondrial DNA in cryoprotectant-treated hard coral (Echinopora spp.) oocytes. (United States)

    Tsai, Sujune; Chen, Jiann-Chu; Spikings, Emma; Li, Jan-Jung; Lin, Chiahsin


    A critical step for successful cryopreservation is to determine the optimal cryoprotectant treatment that can provide protective effects against cryoinjury during freezing and with minimal toxicity. Most cryoprotectants have chemical and osmotic effects when used at high concentrations. Cryoprotectants can damage coral mitochondrial distributions and membrane potentials, which results in reduced ATP production. As mitochondrial DNA (mtDNA) encodes for components of the electron transport chain (ETC) and plays a critical role in ATP synthesis capacity, we determined the effects of cryoprotectants on mtDNA in hard coral (Echinopora spp.) oocytes using quantitative real-time PCR. Our results showed that an insult from a cryoprotectant may be compensated for by the genetic defense mechanisms of these cells. Methanol was found to have the least effect on coral oocytes with regard to their energy status. A single oocyte without cryoprotectant treatment produced an average of 4,220,645 ± 169,990 mtDNA copies, which was greater than that in mammals. However, relatively lower mtDNA copy numbers (<2,000,000) were observed when oocytes were treated with dimethyl sulfoxide (DMSO), propylene glycol (PG), ethylene glycol (EG), or glycerol at a concentration of 3 M for 20 min. These results provide direct evidence that hard coral (Echinopora spp.) oocytes are extremely susceptible to cryoprotectants and support the concerns with regard to the adverse effects of cryoprotectants.

  13. Degradation process of lead chromate in paintings by Vincent van Gogh studied by means of synchrotron X-ray spectromicroscopy and related methods. 1. Artificially aged model samples. (United States)

    Monico, Letizia; Van der Snickt, Geert; Janssens, Koen; De Nolf, Wout; Miliani, Costanza; Verbeeck, Johan; Tian, He; Tan, Haiyan; Dik, Joris; Radepont, Marie; Cotte, Marine


    On several paintings by artists of the end of the 19th century and the beginning of the 20th Century a darkening of the original yellow areas, painted with the chrome yellow pigment (PbCrO(4), PbCrO(4)·xPbSO(4), or PbCrO(4)·xPbO) is observed. The most famous of these are the various Sunflowers paintings Vincent van Gogh made during his career. In the first part of this work, we attempt to elucidate the degradation process of chrome yellow by studying artificially aged model samples. In view of the very thin (1-3 μm) alteration layers that are formed, high lateral resolution spectroscopic methods such as microscopic X-ray absorption near edge (μ-XANES), X-ray fluorescence spectrometry (μ-XRF), and electron energy loss spectrometry (EELS) were employed. Some of these use synchrotron radiation (SR). Additionally, microscopic SR X-ray diffraction (SR μ-XRD), μ-Raman, and mid-FTIR spectroscopy were employed to completely characterize the samples. The formation of Cr(III) compounds at the surface of the chrome yellow paint layers is particularly observed in one aged model sample taken from a historic paint tube (ca. 1914). About two-thirds of the chromium that is present at the surface has reduced from the hexavalent to the trivalent state. The EELS and μ-XANES spectra are consistent with the presence of Cr(2)O(3)·2H(2)O (viridian). Moreover, as demonstrated by μ-XANES, the presence of another Cr(III) compound, such as either Cr(2)(SO(4))(3)·H(2)O or (CH(3)CO(2))(7)Cr(3)(OH)(2) [chromium(III) acetate hydroxide], is likely.

  14. Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil. (United States)

    Song, Mengke; Jiang, Longfei; Zhang, Dayi; Luo, Chunling; Wang, Yan; Yu, Zhiqiang; Yin, Hua; Zhang, Gan


    Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually (13)C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

  15. A paradoxical relationship between Resveratrol and copper (II with respect to degradation of DNA and RNA [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Siddharth Subramaniam


    Full Text Available Resveratrol (R, a plant polyphenol, is known to reduce Cu (II to Cu (I generating reactive oxygen species that can cleave plasmid DNA. Here we report a surprising observation of a paradoxical relationship between R and Cu whereby plasmid DNA cleaving / degrading activity of R-Cu increased progressively as the ratio of R to Cu was increased i.e., the concentration of Cu was successively reduced with respect to a fixed concentration R. Whereas cleavage of plasmid DNA occurred at low molar ratios of R to Cu, at higher ratios, complete degradation of DNA was achieved. By further increasing the ratio, whereby the concentration of Cu was reduced to very low levels, the DNA degrading activity of R-Cu was lost. This paradoxical relationship is also seen with respect to eukaryotic genomic DNA and RNA. Since R-Cu may have anti-cancer and anti-viral activities, our findings may not only help to improve the therapeutic efficacy of R-Cu but also reduce its toxic side effects with the use of low concentration of Cu.

  16. A mathematical model of DNA degradation: Possible role of magnetic nanoparticles

    CERN Document Server

    Binhi, V N


    A mathematical model of genome degradation is proposed that takes into account a variable rate of mutation and increasing number of cells in a developing human organism. The model explains known properties of cancer development, in particular, a synergism between different mutagens and an increased probability of cancer in the early years of life. An iteration equation is suggested that uses only a few model parameters and describes basic regularities observed in cancer onset. In the model context, relatively small chronic variations in the intracellular content of free radicals may markedly affect the probability of a cell to become a cancer cell. On the other hand, magnetic nanoparticles are shown to be an endogenous source of chronic magnetic exposure that increases the local concentration of free radicals. An enhanced level of leukaemia in early childhood is assumed to originate from magnetic nanoparticles located in hematopoietic stem cells.

  17. Modified DOP-PCR for improved STR typing of degraded DNA from human skeletal remains and bloodstains. (United States)

    Ambers, Angie; Turnbough, Meredith; Benjamin, Robert; Gill-King, Harrell; King, Jonathan; Sajantila, Antti; Budowle, Bruce


    Forensic and ancient DNA samples often are damaged and in limited quantity as a result of exposure to harsh environments and the passage of time. Several strategies have been proposed to address the challenges posed by degraded and low copy templates, including a PCR based whole genome amplification method called degenerate oligonucleotide-primed PCR (DOP-PCR). This study assessed the efficacy of four modified versions of the original DOP-PCR primer that retain at least a portion of the 5' defined sequence and alter the number of bases on the 3' end. The use of each of the four modified primers resulted in improved STR profiles from environmentally-damaged bloodstains, contemporary human skeletal remains, American Civil War era bone samples, and skeletal remains of WWII soldiers over those obtained by previously described DOP-PCR methods and routine STR typing. Additionally, the modified DOP-PCR procedure allows for a larger volume of DNA extract to be used, reducing the need to concentrate the sample and thus mitigating the effects of concurrent concentration of inhibitors. Published by Elsevier Ireland Ltd.

  18. Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Risager, Peter Christian; Fahnøe, Ulrik


    . This strategy allows manipulation of viral cDNA by targeted recombination-mediated mutagenesis within bacteria. Results A new CSFV-BAC (pBeloR26) derived from the Riems vaccine strain has been constructed and subsequently modified in the E2 coding sequence, using the targeted recombination strategy to enable......Background Infectious cDNA clones are a prerequisite for directed genetic manipulation of RNA viruses. Here, a strategy to facilitate manipulation and rescue of classical swine fever viruses (CSFVs) from full-length cDNAs present within bacterial artificial chromosomes (BACs) is described...... recombination-mediated mutagenesis provides a powerful tool for expediting the construction of novel RNA genomes and should be applicable to the manipulation of other RNA viruses....

  19. Estimation of age-related DNA degradation from formalin-fixed and paraffin-embedded tissue according to the extraction methods. (United States)

    Watanabe, Mototsugu; Hashida, Shinsuke; Yamamoto, Hiromasa; Matsubara, Takehiro; Ohtsuka, Tomoaki; Suzawa, Ken; Maki, Yuho; Soh, Junichi; Asano, Hiroaki; Tsukuda, Kazunori; Toyooka, Shinichi; Miyoshi, Shinichiro


    Techniques for the extraction and use of nucleic acids from formalin-fixed and paraffin-embedded (FFPE) tissues, preserved over long time periods in libraries, have been developed. However, DNA extracted from FFPE tissues is generally damaged, and long-term storage may affect DNA quality. Therefore, it is important to elucidate the effect of long-term storage on FFPE tissues and evaluate the techniques used to extract DNA from them. In the present study, the yield, purity, and integrity of DNA in FFPE tissue samples was evaluated. Two DNA extraction techniques were used: A silica-binding DNA collection method using QIAamp DNA FFPE Tissue kit (QIA) and a total tissue DNA collection method using a WaxFree DNA extraction kit (WAX). A total of 25 FFPE tissues from lung adenocarcinomas were studied, which had been surgically resected and fixed at Okayama University Hospital prior to examination and subsequent storage at room temperature for 0.5, 3, 6, 9 and 12 years. Extracted DNA was quantified using ultraviolet absorbance, fluorescent dye, and quantitative polymerase chain reaction (qPCR). The quality of the DNA was defined by the absorbance ratio of 260 to 280 nm (A260/280) and Q-score, which is the quantitative value of qPCR product size ratio. The results demonstrated that the yield of total DNA extracted using WAX was significantly greater than when QIA was used (Pextracted using WAX included more contaminants and was significantly more fragmented compared with DNA extracted using QIA (Pextraction (QIA P=0.02, WAX P=0.03; 0.5 years vs. 3 years, QIA Pextraction methods are viable depending on whether high yield or high quality of extracted DNA is required. However, due to the increased degradation with age, storage time limits the available DNA in FFPE tissues regardless of the extraction method.

  20. Targeted rapid amplification of cDNA ends (T-RACE)--an improved RACE reaction through degradation of non-target sequences. (United States)

    Bower, Neil I; Johnston, Ian A


    Amplification of the 5' ends of cDNA, although simple in theory, can often be difficult to achieve. We describe a novel method for the specific amplification of cDNA ends. An oligo-dT adapter incorporating a dUTP-containing PCR primer primes first-strand cDNA synthesis incorporating dUTP. Using the Cap finder approach, another distinct dUTP containing adapter is added to the 3' end of the newly synthesized cDNA. Second-strand synthesis incorporating dUTP is achieved by PCR, using dUTP-containing primers complimentary to the adapter sequences incorporated in the cDNA ends. The double-stranded cDNA-containing dUTP serves as a universal template for the specific amplification of the 3' or 5' end of any gene. To amplify the ends of cDNA, asymmetric PCR is performed using a single gene-specific primer and standard dNTPs. The asymmetric PCR product is purified and non-target transcripts containing dUTP degraded by Uracil DNA glycosylase, leaving only those transcripts produced during the asymmetric PCR. Subsequent PCR using a nested gene-specific primer and the 3' or 5' T-RACE primer results in specific amplification of cDNA ends. This method can be used to specifically amplify the 3' and 5' ends of numerous cDNAs from a single cDNA synthesis reaction.

  1. The α2 helix in the DNA ligase IV BRCT-1 domain is required for targeted degradation of ligase IV during adenovirus infection. (United States)

    Gilson, Timra; Greer, Amy E; Vindigni, Alessandro; Ketner, Gary; Hanakahi, Leslyn A


    In adenovirus E4 mutant infections, viral DNAs form concatemers through a process that requires host Non-homologous End Joining (NHEJ) proteins including DNA Ligase IV (LigIV). Adenovirus proteins E4 34k and E1b 55k form the substrate-selection component of an E3 ubiquitin ligase and prevent concatenation by targeting LigIV for proteasomal degradation. The mechanisms and sites involved in targeting this and other E3 ligase substrates generally are poorly-understood. Through genetic analysis, we identified the α2 helix of one LigIV BRCT domain (BRCT-1) as essential for adenovirus-mediated degradation. Replacement of the BRCT domain of DNA ligase III (LigIII), which is resistant to degradation, with LigIV BRCT-1 does not promote degradation. A humanized mouse LigIV that possesses a BRCT-1 α2 helix identical to the human protein, like its parent, is also resistant to adenovirus-mediated degradation. Thus, both the BRCT-1 α2 helix and an element outside BRCT-1 are required for adenovirus-mediated degradation of LigIV.

  2. Degradation and detection of transgenic Bacillus thuringiensis DNA and proteins in flour of three genetically modified rice events submitted to a set of thermal processes. (United States)

    Wang, Xiaofu; Chen, Xiaoyun; Xu, Junfeng; Dai, Chen; Shen, Wenbiao


    This study aimed to investigate the degradation of three transgenic Bacillus thuringiensis (Bt) genes (Cry1Ab, Cry1Ac, and Cry1Ab/Ac) and the corresponding encoded Bt proteins in KMD1, KF6, and TT51-1 rice powder, respectively, following autoclaving, cooking, baking, or microwaving. Exogenous Bt genes were more stable than the endogenous sucrose phosphate synthase (SPS) gene, and short DNA fragments were detected more frequently than long DNA fragments in both the Bt and SPS genes. Autoclaving, cooking (boiling in water, 30 min), and baking (200 °C, 30 min) induced the most severe Bt protein degradation effects, and Cry1Ab protein was more stable than Cry1Ac and Cry1Ab/Ac protein, which was further confirmed by baking samples at 180 °C for different periods of time. Microwaving induced mild degradation of the Bt and SPS genes, and Bt proteins, whereas baking (180 °C, 15 min), cooking and autoclaving led to further degradation, and baking (200 °C, 30 min) induced the most severe degradation. The findings of the study indicated that degradation of the Bt genes and proteins somewhat correlated with the treatment intensity. Polymerase chain reaction, enzyme-linked immunosorbent assay, and lateral flow tests were used to detect the corresponding transgenic components. Strategies for detecting transgenic ingredients in highly processed foods are discussed.

  3. Improvement of reliability of molecular DNA computing: solution of inverse problem of Raman spectroscopy using artificial neural networks (United States)

    Dolenko, T. A.; Burikov, S. A.; Vervald, E. N.; Efitorov, A. O.; Laptinskiy, K. A.; Sarmanova, O. E.; Dolenko, S. A.


    Elaboration of methods for the control of biochemical reactions with deoxyribonucleic acid (DNA) strands is necessary for the solution of one of the basic problems in the creation of biocomputers—improvement in the reliability of molecular DNA computing. In this paper, the results of the solution of the four-parameter inverse problem of laser Raman spectroscopy—the determination of the type and concentration of each of the DNA nitrogenous bases in multi-component solutions—are presented.

  4. The influence of DNA degradation in formalin-fixed, paraffin-embedded (FFPE) tissue on locus-specific methylation assessment by MS-HRM. (United States)

    Daugaard, Iben; Kjeldsen, Tina E; Hager, Henrik; Hansen, Lise Lotte; Wojdacz, Tomasz K


    Readily accessible formalin-fixed paraffin embedded (FFPE) tissues are a highly valuable source of genetic material for molecular analyses in both research and in vitro diagnostics but frequently genetic material in those samples is highly degraded. With locus-specific methylation changes being widely investigated for use as biomarkers in various aspects of clinical disease management, we aimed to evaluate to what extent standard laboratory procedures can approximate the quality of the DNA extracted from FFPE samples prior to methylation analyses. DNA quality in 107 FFPE non-small cell lung cancer (NSCLC) samples was evaluated using spectrophotometry and gel electrophoresis. Subsequently, the quality assessment results were correlated with the results of locus specific methylation assessment with methylation sensitive high resolution melting (MS-HRM). The correlation of template quality with PCR amplification performance and HRM based methylation detection indicated a significant influence of DNA quality on PCR amplification but not on methylation assessment. In conclusion, standard laboratory procedures fairly well approximate DNA degradation of FFPE samples and DNA degradation does not seem to considerably affect locus-specific methylation assessment by MS-HRM.

  5. Investigation of single nucleotide polymorphism loci susceptible to degradation by ultraviolet light. (United States)

    Machida, Mitsuyo; Taki, Takashi; Shimada, Ryo; Kibayashi, Kazuhiko


    DNA in biological fluids is often degraded by environmental factors. Given that single nucleotide polymorphism (SNP) analyses require shorter amplicons than short tandem repeat (STR) analyses do, their use in human identification using degraded samples has recently attracted attention. Although various SNP loci are used to analyze degraded samples, it is unclear which ones are more appropriate. To characterize and identify SNP loci that are susceptible or resistant to degradation, we artificially degraded DNA, obtained from buccal swabs from 11 volunteers, by exposure to ultraviolet (UV) light for different durations (254 nm for 5, 15, 30, 60, or 120 min) and analyzed the resulting SNP loci. DNA degradation was assessed using gel electrophoresis, STR, and SNP profiling. DNA fragmentation occurred within 5 min of UV irradiation, and successful STR and SNP profiling decreased with increasing duration. However, 73% of SNP loci were still detected correctly in DNA samples irradiated for 120 min, a dose that rendered STR loci undetectable. The unsuccessful SNP typing and the base call failure of nucleotides neighboring the SNPs were traced to rs1031825, and we found that this SNP was susceptible to UV light. When comparing the detection efficiencies of STR and SNP loci, SNP typing was more successful than STR typing, making it effective when using degraded DNA. However, it is important to use rs1031825 with caution when interpreting SNP analyses of degraded DNA.

  6. Artificial ribonucleases. (United States)

    Morrow, J R


    Many inorganic and organic compounds promote the reactions catalyzed by RNase A. Both the transesterification step, where a 2',3'-cyclic phosphate is formed with concomitant cleavage of RNA, and the hydrolysis step, where the 2',3'-cyclic phosphate is converted to a phosphate monoester, may be mimicked with compounds that are readily synthesized in the laboratory. Electrophilic activation of the phosphate ester and charge neutralization are generally important means by which artificial RNases promote phosphate diester displacement reactions. Several artificial RNases operate by a bifunctional general acid/general base mechanism, as does RNase A. Provision of an intramolecular nucleophile appears to be an important pathway for metal complex promoted phosphate diester hydrolysis. In contrast to the successful design of compounds that promote the reactions catalyzed by RNase A, there are no artificial nucleases to date that will cleave the 3' P-O bond of RNA or hydrolyze an oligonucleotide of DNA. Artificial RNases based on both metal complexes and organic compounds have been described. Metal complexes may be particularly effective catalysts for both transesterification and hydrolysis reactions of phosphate diesters. Under physiological conditions (37 degrees C and neutral pH), several metal complexes catalyze the transesterification of RNA. Future work should involve the development of metal complexes which are inert to metal ion release but which maintain open coordination sites for catalytic activity. The design of compounds containing multiple amine or imidazole groups that may demonstrate bifunctional catalysis is a promising route to new artificial RNases. Further design of these compounds and careful placement of catalytic groups may yield new RNase mimics that operate under physiological conditions. The attachment of artificial RNases to recognition agents such as oligodeoxynucleotides to create new sequence-specific endoribonucleases is an exciting field of

  7. Altering an artificial Gagpolnef polyprotein and mode of ENV co-administration affects the immunogenicity of a clade C HIV DNA vaccine.

    Directory of Open Access Journals (Sweden)

    Katharina Böckl

    Full Text Available HIV-1 candidate vaccines expressing an artificial polyprotein comprising Gag, Pol and Nef (GPN and a secreted envelope protein (Env were shown in recent Phase I/II clinical trials to induce high levels of polyfunctional T cell responses; however, Env-specific responses clearly exceeded those against Gag. Here, we assess the impact of the GPN immunogen design and variations in the formulation and vaccination regimen of a combined GPN/Env DNA vaccine on the T cell responses against the various HIV proteins. Subtle modifications were introduced into the GPN gene to increase Gag expression, modify the expression ratio of Gag to PolNef and support budding of virus-like particles. I.m. administration of the various DNA constructs into BALB/c mice resulted in an up to 10-fold increase in Gag- and Pol-specific IFNγ(+ CD8(+ T cells compared to GPN. Co-administering Env with Gag or GPN derivatives largely abrogated Gag-specific responses. Alterations in the molar ratio of the DNA vaccines and spatially or temporally separated administration induced more balanced T cell responses. Whereas forced co-expression of Gag and Env from one plasmid induced predominantly Env-specific T cells responses, deletion of the only H-2(d T cell epitope in Env allowed increased levels of Gag-specific T cells, suggesting competition at an epitope level. Our data demonstrate that the biochemical properties of an artificial polyprotein clearly influence the levels of antigen-specific T cells, and variations in formulation and schedule can overcome competition for the induction of these responses. These results are guiding the design of ongoing pre-clinical and clinical trials.

  8. Assessment of the degradation of polyurethane foams after artificial and natural ageing by using pyrolysis-gas chromatography/mass spectrometry and headspace-solid phase microextraction-gas chromatography/mass spectrometry. (United States)

    Lattuati-Derieux, A; Thao-Heu, S; Lavédrine, B


    Polyurethane foams are widely present in museum collections either as part of the artefacts, or as a material for their conservation. Unfortunately many of PU foam artefacts are in poor condition and often exhibit specific conservation issues. Their fast thermal and photochemical degradations have been the aim of previous researches. It is now accepted that hydrolysis predominates for polyester-based polyurethane PU(ES) whereas oxidation is the principal cause of degradation for polyether-based polyurethane PU(ET) variety. Only a few studies have been devoted to volatile organic compounds (VOCs) emitted by polyurethanes and, to our knowledge, none were performed on polyurethane foams by using headspace-solid phase microextraction (HS-SPME). The objective of the work described here is to assess the impact of some environmental factors (humidity, temperature and daylight) on the degradation of PU foams by evaluating their volatile fractions. We investigated morphological changes, polymerized fractions and volatile fractions of (i) one modern produced PU(ES) foam and one modern PU(ET) foam artificially aged in different conditions as well as (ii) four naturally aged foams collected from various daily life objects and selected for the representativeness of their analytical data. Characterization procedure used was based on attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR), pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) and non-invasive headspace solid-phase microextraction coupled with gas chromatography and mass spectrometry (HS-SPME-GC/MS). In this paper, the formation of alcohol and acid raw products for PU(ES) and glycol derivatives for PU(ET) during natural and artificial ageing is confirmed. These main products can be considered as degradation markers for PU foams. Results show that artificial and natural ageing provide similar analytical results, and confirm that the dominant degradation paths for PU(ES) and for PU(ET) are

  9. PEGylation enhances tumor targeting of plasmid DNA by an artificial cationized protein with repeated RGD sequences, Pronectin. (United States)

    Hosseinkhani, Hossein; Tabata, Yasuhiko


    The objective of this study is to investigate feasibility of a non-viral gene carrier with repeated RGD sequences (Pronectin F+) in tumor targeting for gene expression. The Pronectin F+ was cationized by introducing spermine (Sm) to the hydroxyl groups to allow to polyionically complex with plasmid DNA. The cationized Pronectin F+ prepared was additionally modified with poly(ethylene glycol) (PEG) molecules which have active ester and methoxy groups at the terminal, to form various PEG-introduced cationized Pronectin F+. The cationized Pronectin F+ with or without PEGylation at different extents was mixed with a plasmid DNA of LacZ to form respective cationized Pronectin F+-plasmid DNA complexes. The plasmid DNA was electrophoretically complexed with cationized Pronectin F+ and PEG-introduced cationized Pronectin F+, irrespective of the PEGylation extent, although the higher N/P ratio of complexes was needed for complexation with the latter Pronectin F+. The molecular size and zeta potential measurements revealed that the plasmid DNA was reduced in size to about 250 nm and the charge was changed to be positive by the complexation with cationized Pronectin F+. For the complexation with PEG-introduced cationized Pronectin F+, the charge of complex became neutral being almost 0 mV with the increasing PEGylation extents, while the molecular size was similar to that of cationized Pronectin F+. When cationized Pronectin F+-plasmid DNA complexes with or without PEGylation were intravenously injected to mice carrying a subcutaneous Meth-AR-1 fibrosarcoma mass, the PEG-introduced cationized Pronectin F+-plasmid DNA complex specifically enhanced the level of gene expression in the tumor, to a significantly high extent compared with the cationized Pronectin F+-plasmid DNA complexes and free plasmid DNA. The enhanced level of gene expression depended on the percentage of PEG introduced, the N/P ratio, and the plasmid DNA dose. A fluorescent microscopic study revealed that the

  10. Oral administration of copper to rats leads to increased lymphocyte cellular DNA degradation by dietary polyphenols: implications for a cancer preventive mechanism. (United States)

    Khan, Husain Y; Zubair, Haseeb; Ullah, Mohd F; Ahmad, Aamir; Hadi, Sheikh M


    To account for the observed anticancer properties of plant polyphenols, we have earlier proposed a mechanism which involves the mobilization of endogenous copper ions by polyphenols leading to the generation of reactive oxygen species (ROS) that serve as proximal DNA cleaving agents and lead to cell death. Over the last decade we have proceeded to validate our hypothesis with considerable success. As a further confirmation of our hypothesis, in this paper we first show that oral administration of copper to rats leads to elevated copper levels in lymphocytes. When such lymphocytes with a copper overload were isolated and treated with polyphenols EGCG, genistein and resveratrol, an increased level of DNA breakage was observed. Further, preincubation of lymphocytes having elevated copper levels with the membrane permeable copper chelator neocuproine, resulted in inhibition of polyphenol induced DNA degradation. However, membrane impermeable chelator of copper bathocuproine, as well as iron and zinc chelators were ineffective in causing such inhibition in DNA breakage, confirming the involvement of endogenous copper in polyphenol induced cellular DNA degradation. It is well established that serum and tissue concentrations of copper are greatly increased in various malignancies. In view of this fact, the present results further confirm our earlier findings and strengthen our hypothesis that an important anticancer mechanism of plant polyphenols could be the mobilization of intracellular copper leading to ROS-mediated cellular DNA breakage. In this context, it may be noted that cancer cells are under considerable oxidative stress and increasing such stress to cytotoxic levels could be a successful anticancer approach.

  11. Subtle changes to polymer structure and degradation mechanism enable highly effective nanoparticles for siRNA and DNA delivery to human brain cancer (United States)

    Tzeng, Stephany Y.


    Polymeric materials can be used to deliver nucleic acids such as DNA plasmids and siRNA, but often have low efficacy in human cells. To improve gene delivery, we synthesized an array of over 70 hydrolytically degradable and bioreducible poly(beta-amino ester)s and evaluated properties of over 200 nanoparticle formulations fabricated from these biomaterials. We determined the effect of different polymer structures on the delivery of nucleic acids of different structures and sizes, including siRNA, linear DNA, and circular DNAs (1.8–26 kb). Significantly, leading hydrolytically degradable polymeric nanoparticles delivered DNA to 90±2% of primary human glioblastoma cells with Polymer molecular weight was a driving factor of transfection efficacy for some polymer structures (correlation of r2=0.63) but had no influence on transfection for other structures (r2=0.01). Polymers with a reducible cystamine functional group dramatically improved siRNA delivery by facilitating quick release while generally decreasing DNA delivery compared with non-reducible counterparts (p<0.01). Other material properties facilitated DNA delivery compared to siRNA delivery or increased delivery of both DNA and siRNA. PMID:23184674

  12. Antioxidant properties of neohesperidin dihydrochalcone: inhibition of hypochlorous acid-induced DNA strand breakage, protein degradation, and cell death. (United States)

    Choi, Je-Min; Yoon, Byoung-Seok; Lee, Sang-Kyou; Hwang, Jae-Kwan; Ryang, Ryung


    Neohesperidin dihydrochalcone (NHDC), a non-nutritive sweetening agent, is simply produced by hydrogenation of neohesperidin. The aim of this study is to evaluate the antioxidant and radical scavenging properties of neohesperidin dihydrochalcone and other structurally related compounds (phloridzin, neohesperidin) toward different reactive radical and oxygen species including .ABTS+, .O2-, .OH, H2O2, and HOCl in vitro. NHDC showed remarkable radical scavenging activity against stable radical and reactive oxygen species (ROS) in concentration dependent manner. Especially, NHDC was the most potent inhibitor of H2O2 and HOCl. NHDC showed HOCl scavenging activity of 93.5% and H2O2 scavenging property of 73.5% which was more than those of all the tested compounds including ascorbic acid and BHT. Moreover, NHDC could inhibit protein degradation, plasmid DNA strand cleavage and HIT-T15, HUVEC cell death from HOCl attack while mannitol, BHT, and ascorbic acid could not protect them effectively. These results suggest that NHDC is a potent antioxidant, especially it is evaluated as a novel HOCl scavenger. This study implies the possibility of therapeutic effect of NHDC on ROS-related inflammatory diseases.

  13. Human DNA Ligase I Interacts with and Is Targeted for Degradation by the DCAF7 Specificity Factor of the Cul4-DDB1 Ubiquitin Ligase Complex. (United States)

    Peng, Zhimin; Liao, Zhongping; Matsumoto, Yoshihiro; Yang, Austin; Tomkinson, Alan E


    The synthesis, processing, and joining of Okazaki fragments during DNA replication is complex, requiring the sequential action of a large number of proteins. Proliferating cell nuclear antigen, a DNA sliding clamp, interacts with and coordinates the activity of several DNA replication proteins, including the enzymes flap endonuclease 1 (FEN-1) and DNA ligase I that complete the processing and joining of Okazaki fragments, respectively. Although it is evident that maintaining the appropriate relative stoichiometry of FEN-1 and DNA ligase I, which compete for binding to proliferating cell nuclear antigen, is critical to prevent genomic instability, little is known about how the steady state levels of DNA replication proteins are regulated, in particular the proteolytic mechanisms involved in their turnover. Because DNA ligase I has been reported to be ubiquitylated, we used a proteomic approach to map ubiquitylation sites and screen for DNA ligase I-associated E3 ubiquitin ligases. We identified three ubiquitylated lysine residues and showed that DNA ligase I interacts with and is targeted for ubiquitylation by DCAF7, a specificity factor for the Cul4-DDB1 complex. Notably, knockdown of DCAF7 reduced the degradation of DNA ligase I in response to inhibition of proliferation and replacement of ubiquitylated lysine residues reduced the in vitro ubiquitylation of DNA ligase I by Cul4-DDB1 and DCAF7. In contrast, a different E3 ubiquitin ligase regulates FEN-1 turnover. Thus, although the expression of many of the genes encoding DNA replication proteins is coordinately regulated, our studies reveal that different mechanisms are involved in the turnover of these proteins.

  14. Identification of Enterobacter sakazakii from closely related species: The use of Artificial Neural Networks in the analysis of biochemical and 16S rDNA data

    Directory of Open Access Journals (Sweden)

    Waddington Michael


    Full Text Available Abstract Background Enterobacter sakazakii is an emergent pathogen associated with ingestion of infant formula and accurate identification is important in both industrial and clinical settings. Bacterial species can be difficult to accurately characterise from complex biochemical datasets and computer algorithms can potentially simplify the process. Results Artificial Neural Networks were applied to biochemical and 16S rDNA data derived from 282 strains of Enterobacteriaceae, including 189 E. sakazakii isolates, in order to identify key characteristics which could improve the identification of E. sakazakii. The models developed resulted in a predictive performance for blind (validation data of 99.3 % correct discrimination between E. sakazakii and closely related species for both phenotypic and genotypic data. Three main regions of the partial rDNA sequence were found to be key in discriminating the species. Comparison between E. sakazakii and other strains also constitutively positive for expression of the enzyme α-glucosidase resulted in a predictive performance of 98.7 % for 16S rDNA sequence data and 100% for phenotypic data. Conclusion The computationally based methods developed here show a remarkable ability in reducing data dimensionality and complexity, in order to eliminate noise from the system in order to facilitate the speed and reliability of a potential strain identification system. Furthermore, the approaches described are also able to provide valuable information regarding the population structure and distribution of individual species thus providing the foundations for novel assays and diagnostic tests for rapid identification of pathogens.

  15. Terminal lipophilization of a unique DNA dodecamer by various nucleolipid headgroups: Their incorporation into artificial lipid bilayers and hydrodynamic properties

    Directory of Open Access Journals (Sweden)

    Emma Werz


    Full Text Available A series of six cyanine-5-labeled oligonucleotides (LONs 10–15, each terminally lipophilized with different nucleolipid head groups, were synthesized using the recently prepared phosphoramidites 4b–9b. The insertion of the LONs within an artificial lipid bilayer, composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE, was studied by single molecule fluorescence spectroscopy and microscopy with the help of an optically transparent microfluidic sample carrier with perfusion capabilities. The incorporation of the lipo-oligonucleotides into the bilayer was studied with respect to efficiency (maximal bilayer brightness as well as stability against perfusion (final stable bilayer brightness. Attempts to correlate these parameters with the log P values of the corresponding nucleolipid head groups failed, a result which clearly demonstrates that not only the lipophilicity but mainly the chemical structure and topology of the head group is of decisive importance for the optimal interaction of a lipo-oligonucleotide with an artificial lipid bilayer. Moreover, fluorescence half-live and diffusion time values were measured to determine the diffusion coefficients of the lipo-oligonucleotides.

  16. Development and Application of a Transformation-competent Artificial chromosome (TAC) Genomic DNA Library in Allotetrapolid Cotton (Gossypium hirsutum L. )%陆地棉TAC基因组DNA文库的构建及利用

    Institute of Scientific and Technical Information of China (English)

    Xiao-e LIANG; Jin-feng SUO; Yong-biao XUE


    @@ The technology of cloning and transferring of large DNA fragments in plants is important for high-efficient identification of new genes and study of gene functions. Tranformationcompetent artificial chromosome (TAC) vector system has been shown to be very useful for efficient gene isolation in Arobidopsis thaliana.

  17. Spectral, thermal, kinetic, molecular modeling and eukaryotic DNA degradation studies for a new series of albendazole (HABZ) complexes (United States)

    El-Metwaly, Nashwa M.; Refat, Moamen S.


    This work represents the elaborated investigation for the ligational behavior of the albendazole ligand through its coordination with, Cu(II), Mn(II), Ni(II), Co(II) and Cr(III) ions. Elemental analysis, molar conductance, magnetic moment, spectral studies (IR, UV-Vis and ESR) and thermogravimetric analysis (TG and DTG) have been used to characterize the isolated complexes. A deliberate comparison for the IR spectra reveals that the ligand coordinated with all mentioned metal ions by the same manner as a neutral bidentate through carbonyl of ester moiety and NH groups. The proposed chelation form for such complexes is expected through out the preparation conditions in a relatively acidic medium. The powder XRD study reflects the amorphous nature for the investigated complexes except Mn(II). The conductivity measurements reflect the non-electrolytic feature for all complexes. In comparing with the constants for the magnetic measurements as well as the electronic spectral data, the octahedral structure was proposed strongly for Cr(III) and Ni(II), the tetrahedral for Co(II) and Mn(II) complexes but the square-pyramidal for the Cu(II) one. The thermogravimetric analysis confirms the presence or absence of water molecules by any type of attachments. Also, the kinetic parameters are estimated from DTG and TG curves. ESR spectrum data for Cu(II) solid complex confirms the square-pyramidal state is the most fitted one for the coordinated structure. The albendazole ligand and its complexes are biologically investigated against two bacteria as well as their effective effect on degradation of calf thymus DNA.

  18. Apoptotic DNA Degradation into Oligonucleosomal Fragments, but Not Apoptotic Nuclear Morphology, Relies on a Cytosolic Pool of DFF40/CAD Endonuclease* (United States)

    Iglesias-Guimarais, Victoria; Gil-Guiñon, Estel; Gabernet, Gisela; García-Belinchón, Mercè; Sánchez-Osuna, María; Casanelles, Elisenda; Comella, Joan X.; Yuste, Victor J.


    Apoptotic cell death is characterized by nuclear fragmentation and oligonucleosomal DNA degradation, mediated by the caspase-dependent specific activation of DFF40/CAD endonuclease. Here, we describe how, upon apoptotic stimuli, SK-N-AS human neuroblastoma-derived cells show apoptotic nuclear morphology without displaying concomitant internucleosomal DNA fragmentation. Cytotoxicity afforded after staurosporine treatment is comparable with that obtained in SH-SY5Y cells, which exhibit a complete apoptotic phenotype. SK-N-AS cell death is a caspase-dependent process that can be impaired by the pan-caspase inhibitor q-VD-OPh. The endogenous inhibitor of DFF40/CAD, ICAD, is correctly processed, and dff40/cad cDNA sequence does not reveal mutations altering its amino acid composition. Biochemical approaches show that both SH-SY5Y and SK-N-AS resting cells express comparable levels of DFF40/CAD. However, the endonuclease is poorly expressed in the cytosolic fraction of healthy SK-N-AS cells. Despite this differential subcellular distribution of DFF40/CAD, we find no differences in the subcellular localization of both pro-caspase-3 and ICAD between the analyzed cell lines. After staurosporine treatment, the preferential processing of ICAD in the cytosolic fraction allows the translocation of DFF40/CAD from this fraction to a chromatin-enriched one. Therefore, the low levels of cytosolic DFF40/CAD detected in SK-N-AS cells determine the absence of DNA laddering after staurosporine treatment. In these cells DFF40/CAD cytosolic levels can be restored by the overexpression of their own endonuclease, which is sufficient to make them proficient at degrading their chromatin into oligonucleosome-size fragments after staurosporine treatment. Altogether, the cytosolic levels of DFF40/CAD are determinants in achieving a complete apoptotic phenotype, including oligonucleosomal DNA degradation. PMID:22253444

  19. Is passive transmission of non-viral vectors through artificial insemination of sperm-DNA mixtures sufficient for chicken transgenesis?


    CHAPARIAN, Shahram; ABDULAHNEJAD, Ahad; RASHIDI, Farzad; Toghyani, Majid; Gheisari, Abbasali; Eghbalsaied, Shahin


    DNA uptake in the post-acrosomal region of the spermatozoa takes place exclusively in immotile spermatozoa that are naturally unable to fertilize eggs. The present study aimed to assess whether passive transmission of non-viral vectors to the surrounding areas of chicken embryos could be an alternate mechanism in chicken sperm-mediated gene transfer. First, the presence of nucleases in rooster seminal plasma was evaluated. Semen ejaculates from five roosters were centrifuged and the supernata...

  20. Artificial intelligence

    CERN Document Server

    Hunt, Earl B


    Artificial Intelligence provides information pertinent to the fundamental aspects of artificial intelligence. This book presents the basic mathematical and computational approaches to problems in the artificial intelligence field.Organized into four parts encompassing 16 chapters, this book begins with an overview of the various fields of artificial intelligence. This text then attempts to connect artificial intelligence problems to some of the notions of computability and abstract computing devices. Other chapters consider the general notion of computability, with focus on the interaction bet

  1. Chitosan/Fe spheres on the blue QR-19 dye degradation by photo Fenton processes using artificial or solar light; Esferas de quitosana/Fe na degradacao do corante azul QR-19 por processos foto-Fenton utilizando luz artificial ou solar

    Energy Technology Data Exchange (ETDEWEB)

    Souza, Kely V. de; Zamora, Patricio G.P.; Zawadzki, Sonia F. [Universidade Federal do Parana (DQ/UFPR), Curitiba, PR (Brazil). Dept. de Quimica], E-mail:


    The contamination of water resources is one of the greatest environmental problems today. Among the polluting sources are the textile industries due to the production of large volumes of effluent, often treated inefficiently. The main reason for the environmental impact of the rejected materials is the presence of dyes such as azo reactive compounds that can generate by-products with carcinogenic and mutagenic effects. They may also include anthraquinone type compounds, which are highly resistant to degradation and persist in the effluent for a long time. The purpose of this study is the use of photo-Fenton processes assisted by artificial or solar light, using immobilized iron on chitosan beads, crosslinked with glutaraldehyde, for the anthraquinone type compound Blue QR-19 standard dye degradation in aqueous solutions. The obtained spheres showed a regular size and 4.0 mm diameter. The results showed 90% discoloration of the system within 180 minutes and a 60% total organic carbon (TOC)reduction for the photo-Fenton system using artificial light. For the system using sunlight, the total discoloration was achieved in 120 minutes and the TOC value decreased 70%. Also observed was that iron remained in the polymeric matrix after the treatment, thus allowing reuse. (author)

  2. An approach to utilize the artificial high power LED UV-A radiation in photoreactors for the degradation of methylene blue. (United States)

    Betancourt-Buitrago, L A; Vásquez, C; Veitia, L; Ossa-Echeverry, O; Rodriguez-Vallejo, J; Barraza-Burgos, J; Marriaga-Cabrales, N; Machuca-Martínez, F


    Utilization of UV LED light is trending in the development of photoreactors for pollutant treatment. In this study, two different geometries were studied in the degradation of methylenebBlue (MB) using high power UVA LED as a source of light. The dosage, initial concentration, electric power, and H2O2 addition were evaluated in the two geometries: a mini CPC (Cilindrical Parabolic Collector) and a vertical cylindrical with external irradiation both coupled with LED UVA. Best degradation was obtained for 0.3 g L(-1) TiO2, 40 min, and 15 ppm of MB of initial concentration in the standard batch reactor. It was found that the best system was a cpc geometry. Also, hydrogen peroxide was used as an electron acceptor and 97% degradation was obtained in 30 min with 10 mM H2O2 and 0.4 g TiO2/L. Power of the LEDs was also evaluated and it was found that 20 W m(-2) is the best operational condition to achieve the best MB degradation avoiding the oxidant species recombination.

  3. Hepatitis C virus core protein inhibits E6AP expression via DNA methylation to escape from ubiquitin-dependent proteasomal degradation. (United States)

    Kwak, Juri; Shim, Joo Hee; Tiwari, Indira; Jang, Kyung Lib


    The E6-associated protein (E6AP) is a ubiquitin ligase that mediates ubiquitination and proteasomal degradation of hepatitis C virus (HCV) core protein. Given the role of HCV core protein as a major component of the viral nucleocapsid, as well as a multifunctional protein involved in viral pathogenesis and hepatocarcinogenesis, HCV has likely evolved a strategy to counteract the host anti-viral defense mechanism of E6AP and maximize its potential to produce infectious virus particles. In the present study, we found that HCV core protein derived from either ectopic expression or HCV infection inhibits E6AP expression via promoter hypermethylation in human hepatocytes. As a result, the potential of E6AP to ubiquitinate and degrade HCV core protein through the ubiquitin-proteasome system was severely impaired, which in turn led to stimulation of virus propagation. The effects of HCV core protein were almost completely abolished when the E6AP level was restored by ectopic expression of E6AP, treatment with a universal DNA methyltransferase (DNMT) inhibitor, 5-Aza-2'dC, or knock-down of DNMT1. In conclusion, HCV core protein inhibits E6AP expression via DNA methylation to protect itself from ubiquitin-dependent proteasomal degradation and stimulate virus propagation, providing a potential target for the development of anti-viral drugs against HCV.

  4. The comparison of naturally weathered oil and artificially photo-degraded oil at the molecular level by a combination of SARA fractionation and FT-ICR MS

    Energy Technology Data Exchange (ETDEWEB)

    Islam, Ananna; Cho, Yunju [Kyungpook National University, Department of Chemistry, Daegu 702-701 (Korea, Republic of); Yim, Un Hyuk; Shim, Won Joon [Oil and POPs Research Group, Korea Institute of Ocean Science and Technology, Geoje 656-834 (Korea, Republic of); Kim, Young Hwan [Division of Mass Spectrometry Research and Center for Analytical Research in Disease Sciences, Korea Basic Science Institute, Ochang 863-883 (Korea, Republic of); Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Kim, Sunghwan, E-mail: [Kyungpook National University, Department of Chemistry, Daegu 702-701 (Korea, Republic of); Division of Mass Spectrometry Research and Center for Analytical Research in Disease Sciences, Korea Basic Science Institute, Ochang 863-883 (Korea, Republic of)


    Highlights: • Weathered oils from the Hebei Spirit oil spill and photo degraded oils are compared. • We investigate changes of polar species at the molecular level by 15T FT-ICR MS. • Significant reduction of sulfur class compounds in saturates fraction is observed. • The relative abundance of protonated compounds (presumably basic nitrogen compounds) increase after degradation. • Changes of polar compounds occurred by natural and photo degradation are similar. -- Abstract: Two sets of oil samples, one obtained from different weathering stages of the M/V Hebei Spirit oil spill site and the other prepared by an in vitro photo-degradation experiment, were analyzed and compared at the molecular level by atmospheric pressure photo-ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). For a more detailed comparison at the molecular level, the oil samples were separated into saturate, aromatic, resin, and asphaltene (SARA) fractions before MS analysis. Gravimetric analysis of the SARA fractions revealed a decreased weight percentage of the aromatic fraction and an increased resin fraction in both sets of samples. Molecular-level investigations of the SARA fractions showed a significant reduction in the S{sub 1} class in the saturate fraction and increase of S{sub 1}O{sub 1} class compounds with high DBE values in resin fraction. Levels of N{sub 1} and N{sub 1}O{sub 1} class compounds resulting in protonated ions (presumably basic nitrogen compounds) increased after degradation compared to compounds generating molecular ions (presumably non-basic nitrogen compounds). This study revealed changes occurring in heteroatom polar species of crude oils such as sulfur and nitrogen containing compounds that have not been easily detected with conventional GC based techniques.

  5. Cigarette smoke induces proteasomal-mediated degradation of DNA methyltransferases and methyl CpG-/CpG domain-binding proteins in embryonic orofacial cells. (United States)

    Mukhopadhyay, Partha; Greene, Robert M; Pisano, M Michele


    Orofacial clefts, the most prevalent of developmental anomalies, occur with a frequency of 1 in 700 live births. Maternal cigarette smoking during pregnancy represents a risk factor for having a child with a cleft lip and/or cleft palate. Using primary cultures of first branchial arch-derived cells (1-BA cells), which contribute to the formation of the lip and palate, the present study addressed the hypothesis that components of cigarette smoke alter global DNA methylation, and/or expression of DNA methyltransferases (Dnmts) and various methyl CpG-binding proteins. Primary cultures of 1-BA cells, exposed to 80μg/mL cigarette smoke extract (CSE) for 24h, exhibited a >13% decline in global DNA methylation and triggered proteasomal-mediated degradation of Dnmts (DNMT-1 and -3a), methyl CpG binding protein 2 (MeCP2) and methyl-CpG binding domain protein 3 (MBD-3). Pretreatment of 1-BA cells with the proteasomal inhibitor MG-132 completely reversed such degradation. Collectively, these data allow the suggestion of a potential epigenetic mechanism underlying maternal cigarette smoke exposure-induced orofacial clefting. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Phosphorylation of Hdmx mediates its Hdm2- and ATM-dependent degradation in response to DNA damage


    Pereg, Yaron; Shkedy, Dganit; de Graaf, Petra; Meulmeester, Erik; Edelson-Averbukh, Marina; Salek, Mogjiborahman; Biton, Sharon; Teunisse, Amina F.A.S.; Lehmann, Wolf D.; Jochemsen, Aart G.; Shiloh, Yosef


    Maintenance of genomic stability depends on the DNA damage response, an extensive signaling network that is activated by DNA lesions such as double-strand breaks (DSBs). The primary activator of the mammalian DSB response is the nuclear protein kinase ataxia–telangiectasia, mutated (ATM), which phosphorylates key players in various arms of this network. The activation and stabilization of the p53 protein play a major role in the DNA damage response and are mediated by ATM-dependent posttransl...

  7. Artificial Intelligence. (United States)

    Waltz, David L.


    Describes kinds of results achieved by computer programs in artificial intelligence. Topics discussed include heuristic searches, artificial intelligence/psychology, planning program, backward chaining, learning (focusing on Winograd's blocks to explore learning strategies), concept learning, constraint propagation, language understanding…

  8. γ-H2AX as a biomarker of DNA damage induced by ionizing radiation in human peripheral blood lymphocytes and artificial skin (United States)

    Redon, Christophe E.; Dickey, Jennifer S.; Bonner, William M.; Sedelnikova, Olga A.


    Ionizing radiation (IR) exposure is inevitable in our modern society and can lead to a variety of deleterious effects including cancer and birth defects. A reliable, reproducible and sensitive assessment of exposure to IR and the individual response to that exposure would provide much needed information for the optimal treatment of each donor examined. We have developed a diagnostic test for IR exposure based on detection of the phosphorylated form of variant histone H2AX (γ-H2AX), which occurs specifically at sites of DNA double-strand breaks (DSBs). The cell responds to a nascent DSB through the phosphorylation of thousands of H2AX molecules flanking the damaged site. This highly amplified response can be visualized as a γ-H2AX focus in the chromatin that can be detected in situ with the appropriate antibody. Here we assess the usability of γ-H2AX focus formation as a possible biodosimeter for human exposure to IR using peripheral blood lymphocytes irradiated ex vivo and three-dimensional artificial models of human skin biopsies. In both systems, the tissues were exposed to 0.2–5 Gy, doses of IR that might be realistically encountered in various scenarios such as cancer radiotherapies or accidental exposure to radiation. Since the γ-H2AX response is maximal 30 minutes after exposure and declines over a period of hours as the cells repair the damage, we examined the time limitations of the useful detectibility of γ-H2AX foci. We report that a linear response proportional to the initial radiation dose was obtained 48 hours and 24 hours after exposure in blood samples and skin cells respectively. Thus, detection of γ-H2AX formation to monitor DNA damage in minimally invasive blood and skin tests could be useful tools to determine radiation dose exposure and analyze its effects on humans. PMID:20046946

  9. Research on the Preparation of Bacterial Artificial Chromosome Library Genomic DNA%细菌人工染色体文库基因组DNA制备技术

    Institute of Scientific and Technical Information of China (English)

    陈献伟; 王会; 关伟军; 高剑峰


    试验旨在对基因组DNA的制备进行研究,为细菌人工染色体(bacterial artificial charomosome,BAc)文库的构建奠定基础.以豁眼鹅全血为试验材料,提取高质量的基因组DNA,分别采用Hind Ⅲ、EcoR Ⅰ和BamHⅠ3种限制性内切酶对所提基因组DNA进行部分酶切,并利用控制酶切时间、设置不同的Hind Ⅲ酶切浓度梯度对基因组DNA进行部分酶切.结果表明,Hind Ⅲ为最佳限制性内切酶,并得到了最佳酶切用量(40U/μL).该方法所制备的基因组DNA质量较好,可用于BAC文库的构建.

  10. A high-efficient batch-recirculated photoreactor packed with immobilized TiO2-P25 nanoparticles onto glass beads for photocatalytic degradation of phenazopyridine as a pharmaceutical contaminant: artificial neural network modeling. (United States)

    Shargh, Mahdie; Behnajady, Mohammad A


    In this study, removal efficiency of phenazopyridine (PhP) as a model pharmaceutical contaminant was investigated in a batch-recirculated photoreactor packed with immobilized TiO2-P25 nanoparticles on glass beads. Influence of various operational parameters such as irradiation time, initial concentration of PhP, volume of solution, volumetric flow rate, pH and power of light source was investigated. Results indicated that removal percentage increases with the rise of irradiation time, volumetric flow rate and power of light source but decreases with the rise of initial concentration of PhP and volume of solution. Highest removal percentage was obtained in the natural pH of PhP solution (pH = 5.9). Results of mineralization studies also showed a decreasing trend of total organic carbon (TOC) and producing mineralization products such as NO3(-), NO2(-) and NH4(+). Modeling of the process using artificial neural network showed that the most effective parameters in the degradation of PhP were volume of solution and power of light source. The packed bed photoreactor with TiO2-P25 nanoparticles coated onto glass beads in consecutive repeats have the proper ability for PhP degradation. Therefore, this system can be a promising alternative for the removal of recalcitrant organic pollutants such as PhP from aqueous solutions.

  11. A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection

    Directory of Open Access Journals (Sweden)

    Tetreau Guillaume


    Full Text Available Abstract Background For most organisms, developing hundreds of genetic markers spanning the whole genome still requires excessive if not unrealistic efforts. In this context, there is an obvious need for methodologies allowing the low-cost, fast and high-throughput genotyping of virtually any species, such as the Diversity Arrays Technology (DArT. One of the crucial steps of the DArT technique is the genome complexity reduction, which allows obtaining a genomic representation characteristic of the studied DNA sample and necessary for subsequent genotyping. In this article, using the mosquito Aedes aegypti as a study model, we describe a new genome complexity reduction method taking advantage of the abundance of miniature inverted repeat transposable elements (MITEs in the genome of this species. Results Ae. aegypti genomic representations were produced following a two-step procedure: (1 restriction digestion of the genomic DNA and simultaneous ligation of a specific adaptor to compatible ends, and (2 amplification of restriction fragments containing a particular MITE element called Pony using two primers, one annealing to the adaptor sequence and one annealing to a conserved sequence motif of the Pony element. Using this protocol, we constructed a library comprising more than 6,000 DArT clones, of which at least 5.70% were highly reliable polymorphic markers for two closely related mosquito strains separated by only a few generations of artificial selection. Within this dataset, linkage disequilibrium was low, and marker redundancy was evaluated at 2.86% only. Most of the detected genetic variability was observed between the two studied mosquito strains, but individuals of the same strain could still be clearly distinguished. Conclusion The new complexity reduction method was particularly efficient to reveal genetic polymorphisms in Ae. egypti. Overall, our results testify of the flexibility of the DArT genotyping technique and open new

  12. Autosomal and Y-STR analysis of degraded DNA from the 120-year-old skeletal remains of Ezekiel Harper. (United States)

    Ambers, Angie; Gill-King, Harrell; Dirkmaat, Dennis; Benjamin, Robert; King, Jonathan; Budowle, Bruce


    The 120-year-old skeletal remains of Confederate Civil War soldier Captain Ezekiel "Zeke" Harper were exhumed by court order in January 2011 for DNA analysis. The goal of the DNA testing was to support or refute whether Captain Harper had fathered a son (Earl J. Maxwell) with his Native American maid prior to his murder in 1892. Bones with adequate structural integrity (left tibia, right tibia, right femur, mandible, four teeth) were retrieved from the burial site and sent to the Institute of Applied Genetics in Fort Worth, Texas for analysis. Given the age and condition of the remains, three different extraction methods were used to maximize the probability of DNA recovery. The majority of the DNA isolates from over fifty separate bone sections yielded partial autosomal STR genotypes and partial Y-STR haplotypes. After comparing the partial results for concordance, consensus profiles were generated for comparison to reference samples from alleged family members. Considering the genetic recombination that occurs in autosomal DNA over the generations within a family, Y-STR analysis was determined to be the most appropriate and informative approach for determining potential kinship. Two of Earl J. Maxwell's grandsons submitted buccal samples for comparison. The Y-STR haplotypes obtained from both of these reference samples were identical to each other and to the alleles in Ezekiel Harper's consensus profile at all 17 loci examined. This Y-STR haplotype was not found in either of two major Y-STR population databases (U.S. Y-STR database and YHRD). The fact that the Y-STR haplotype obtained from Ezekiel's skeletal remains and Earl's grandsons is not found in either population database demonstrates its rarity and further supports a paternal lineage relationship among them. Results of the genetic analyses are consistent with the hypothesis that Earl J. Maxwell is the son of Ezekiel Harper.

  13. Diagnosis and Prognostication of Ductal Adenocarcinomas of the Pancreas Based on Genome-Wide DNA Methylation Profiling by Bacterial Artificial Chromosome Array-Based Methylated CpG Island Amplification

    Directory of Open Access Journals (Sweden)

    Masahiro Gotoh


    Full Text Available To establish diagnostic criteria for ductal adenocarcinomas of the pancreas (PCs, bacterial artificial chromosome (BAC array-based methylated CpG island amplification was performed using 139 tissue samples. Twelve BAC clones, for which DNA methylation status was able to discriminate cancerous tissue (T from noncancerous pancreatic tissue in the learning cohort with a specificity of 100%, were identified. Using criteria that combined the 12 BAC clones, T-samples were diagnosed as cancers with 100% sensitivity and specificity in both the learning and validation cohorts. DNA methylation status on 11 of the BAC clones, which was able to discriminate patients showing early relapse from those with no relapse in the learning cohort with 100% specificity, was correlated with the recurrence-free and overall survival rates in the validation cohort and was an independent prognostic factor by multivariate analysis. Genome-wide DNA methylation profiling may provide optimal diagnostic markers and prognostic indicators for patients with PCs.

  14. Determinación por Visión Artificial del Factor de Degradación en Aleaciones Biocompatibles Computer Vision for Determination of Degradation Factor in Biocompatible Alloys

    Directory of Open Access Journals (Sweden)

    Willian Aperador-Chaparro


    Full Text Available Se determinó por visión artificial el factor de degradación de una aleación biocompatible, AISI 316LVM. Para ello, se utilizó una solución fisiológica simulada (solución de Hanks, electrolito que simula la composición presente en el organismo, es decir, el ambiente donde el implante se utilizará. El comportamiento electroquímico fue evaluado mediante curvas potencio-dinámicas. La caracterización superficial se desarrolló mediante un estereoscopio y los productos de corrosión se evaluaron mediante difracción de rayos X. El sistema usó una imagen microscópica de la superficie del material en su estado natural (brillo espejo como parámetro base para la comparación, para definir en qué estado se encuentran las muestras una vez han pasado por las pruebas realizadas. Se encontró, que es posible estimar el factor de degradación o de deterioro en un material mediante un análisis topográfico del mismo.The degradation factor of a biocompatible alloy, AISI 316LVM, was determined by computer vision. For this, a simulated physiological solution (Hanks' solution which simulates the electrolyte composition in the body, that is the environment in which the implant is used. The electrochemical behavior was evaluated by potentio-dynamic curves. The surface characterization was performed using a stereoscope and corrosion products were evaluated by X-ray diffraction. The system used a microscopic image of the surface of the material in its natural state (mirror finish as a basis for comparison parameter to define what state are once samples have undergone testing. It was found that it is possible to estimate the factor of degradation or deterioration of a material through a topographic analysis.

  15. Artificial blood

    Directory of Open Access Journals (Sweden)

    Sarkar Suman


    Full Text Available Artificial blood is a product made to act as a substitute for red blood cells. While true blood serves many different functions, artificial blood is designed for the sole purpose of transporting oxygen and carbon dioxide throughout the body. Depending on the type of artificial blood, it can be produced in different ways using synthetic production, chemical isolation, or recombinant biochemical technology. Development of the first blood substitutes dates back to the early 1600s, and the search for the ideal blood substitute continues. Various manufacturers have products in clinical trials; however, no truly safe and effective artificial blood product is currently marketed. It is anticipated that when an artificial blood product is available, it will have annual sales of over $7.6 billion in the United States alone.

  16. Artificial blood. (United States)

    Sarkar, Suman


    Artificial blood is a product made to act as a substitute for red blood cells. While true blood serves many different functions, artificial blood is designed for the sole purpose of transporting oxygen and carbon dioxide throughout the body. Depending on the type of artificial blood, it can be produced in different ways using synthetic production, chemical isolation, or recombinant biochemical technology. Development of the first blood substitutes dates back to the early 1600s, and the search for the ideal blood substitute continues. Various manufacturers have products in clinical trials; however, no truly safe and effective artificial blood product is currently marketed. It is anticipated that when an artificial blood product is available, it will have annual sales of over $7.6 billion in the United States alone.

  17. Evidence of apoptotic effects of 2,4-D and butachlor on walking catfish, Clarias batrachus, by transmission electron microscopy and DNA degradation studies. (United States)

    Ateeq, Bushra; Farah, M Abul; Ahmad, Waseem


    Apoptosis or programmed cell death is characterized morphologically by chromatin condensation, cell shrinkage, fragmentation of the nucleus and cytoplasm, and consequently formation of apoptotic bodies. It has also been best characterized by the cleavage of DNA into nucleosomal size fragments of 180-200 bp or multiples of the same. Contrary to this, under extreme conditions, the cells were found to show adaptive response to apoptosis and unable to regulate their own death; necrosis is therefore predominantly observed. In the present study, we showed induction of apoptosis in Clarias batrachus due to sublethal concentration of 2,4-D and butachlor at multiple exposure time. The first phase of the study involved light microscopy (LM) and transmission electron microscopy (TEM) for ultrastructural abnormalities of the germinal tissues. While, in the second phase of the study, DNA degradation of blood and hepatic tissue was resolved on agarose gel electrophoresis. In histopathological studies, large numbers of stage II oocytes were noted for nuclear blebbing irrespective of the test chemical. Some of the butachlor-exposed oocytes showed vacuolation and electron dense cytoplasm along with thickened nuclear envelope, having close association with the lysosomes on the cytoplasmic side. Some oocytes undergo nuclear blebbing having inner dense core and translucent cytoplasm. Leydig cells were slightly hypertrophied and few appeared pycnotic, a process involving necrotic changes in which the cell nuclei were characterized by rounding up and condensation resulting in hyperchromatic staining or pycnosis. In testicular tissue, spermatogonial nuclei had irregular large clumps of heterochromatin adjoining the nuclear membrane indicating initial stage of apoptotic cell death. Electrophoretic separation resulted in a ladder pattern of blood DNA and smear like pattern of hepatic DNA. These results indicate that the above herbicides are able to induce apoptosis both at molecular as

  18. DNA rearrangement has occurred in the carbazole-degradative plasmid pCAR1 and the chromosome of its unsuitable host, Pseudomonas fluorescens Pf0-1. (United States)

    Shintani, Masaki; Matsumoto, Takashi; Yoshikawa, Hirofumi; Yamane, Hisakazu; Ohkuma, Moriya; Nojiri, Hideaki


    The carbazole-degradative plasmid pCAR1 carries the class II transposon Tn4676, which contains the car and ant genes, essential for conversion of carbazole into anthranilate, and anthranilate into catechol, respectively. In our previous study, DNA rearrangements in pCAR1 were frequently detected in the host Pseudomonas fluorescens Pf0-1 in the presence of carbazole, resulting in the improvement of host survivability. Several Pf0-1 mutants harbouring pCAR1 were isolated, and deletion of DNA in the plasmid ant gene was found. Here, we compared genome sequences of the parent strain Pf0-1L(pCAR1::rfp) and one of its mutants, 5EP83, to assess whether other DNA rearrangements occurred in either the plasmid or the host chromosome. We found transposition of Tn4676 into the 5EP83 chromosome. In addition, ISPre1 had transposed into the car gene intergenic region on the pCAR1-derivative plasmid of 5EP83, which inhibited car transcription. As a result of these transpositions, 5EP83 was able to metabolize carbazole due to the Tn4676 on its chromosome, although the car genes on its plasmid were non-functional. We also found that one copy of duplicate carAa genes had been deleted, and that ISPre4 had transposed into both the host chromosome and the plasmid. Our findings suggest that Pf0-1 harbouring pCAR1 is subjected to DNA rearrangements not only on the plasmid but also on its chromosome in the presence of carbazole.

  19. DNA (United States)

    Stent, Gunther S.


    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)

  20. Esferas de quitosana/Fe na degradação do corante Azul QR-19 por processos foto-Fenton utilizando luz artificial ou solar Chitosan/Fe spheres on the Blue QR-19 dye degradation by photo Fenton processes using artificial or solar light

    Directory of Open Access Journals (Sweden)

    Kely V. de Souza


    Full Text Available A contaminação dos recursos hídricos é um dos maiores problemas ambientais da atualidade. Dentre as várias fontes poluidoras, destacam-se as indústrias têxteis, por serem fontes geradoras de grandes volumes de efluentes, muitas vezes tratados de maneira ineficiente. A principal causa do grande impacto ambiental decorrente deste descarte é a presença dos corantes, tais como os compostos do tipo azo, que podem gerar subprodutos de caráter carcinogênico e/ou mutagênico, ou como os de base antraquinona, que são muito resistentes à degradação natural e portanto persistem no efluente por um longo tempo. O objetivo do presente trabalho consiste na utilização de processos foto-Fenton assistidos por luz artificial e solar, utilizando ferro imobilizado em esferas de quitosana reticulada com glutaraldeído, para promover a degradação do corante reativo Azul QR-19, de base antraquinona, em solução aquosa. As esferas obtidas apresentaram tamanho regular com diâmetro de 4,0 mm. Os resultados demonstraram 90% de descoloração do sistema em 180minutos e redução de 60% do teor de carbono orgânico total (COT, para o sistema foto-Fenton utilizando luz artificial. Para o sistema fotoassistido com luz solar, a descoloração foi integralmente obtida em 120 minutos com 70% de redução do teor de COT. Foi observado que o ferro permaneceu na matriz após o tratamento, possibilitando sua reutilização.The contamination of water resources is one of the greatest environmental problems today. Among the polluting sources are the textile industries due to the production of large volumes of effluent, often treated inefficiently. The main reason for the environmental impact of the rejected materials is the presence of dyes such as azo reactive compounds that can generate by-products with carcinogenic and mutagenic effects. They may also include anthraquinone type compounds, which are highly resistant to degradation and persist in the effluent for a

  1. DNA degradation in genetically modified rice with Cry1Ab by food processing methods: implications for the quantification of genetically modified organisms. (United States)

    Xing, Fuguo; Zhang, Wei; Selvaraj, Jonathan Nimal; Liu, Yang


    Food processing methods contribute to DNA degradation, thereby affecting genetically modified organism detection and quantification. This study evaluated the effect of food processing methods on the relative transgenic content of genetically modified rice with Cry1Ab. In steamed rice and rice noodles, the levels of Cry1Ab were ⩾ 100% and <83%, respectively. Frying and baking in rice crackers contributed to a reduction in Pubi and Cry1Ab, while microwaving caused a decrease in Pubi and an increase in Cry1Ab. The processing methods of sweet rice wine had the most severe degradation effects on Pubi and Cry1Ab. In steamed rice and rice noodles, Cry1Ab was the most stable, followed by SPS and Pubi. However, in rice crackers and sweet rice wine, SPS was the most stable, followed by Cry1Ab and Pubi. Therefore, Cry1Ab is a better representative of transgenic components than is Pubi because the levels of Cry1Ab were less affected compared to Pubi. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. DNA stable-isotope probing of oil sands tailings pond enrichment cultures reveals different key players for toluene degradation under methanogenic and sulfidogenic conditions. (United States)

    Laban, Nidal Abu; Dao, Anh; Foght, Julia


    Oil sands tailings ponds are anaerobic repositories of fluid wastes produced by extraction of bitumen from oil sands ores. Diverse indigenous microbiota biodegrade hydrocarbons (including toluene) in situ, producing methane, carbon dioxide and/or hydrogen sulfide, depending on electron acceptor availability. Stable-isotope probing of cultures enriched from tailings associated specific taxa and functional genes to (13)C6- and (12)C7-toluene degradation under methanogenic and sulfate-reducing conditions. Total DNA was subjected to isopycnic ultracentrifugation followed by gradient fraction analysis using terminal restriction fragment length polymorphism (T-RFLP) and construction of 16S rRNA, benzylsuccinate synthase (bssA) and dissimilatory sulfite reductase (dsrB) gene clone libraries. T-RFLP analysis plus sequencing and in silico digestion of cloned taxonomic and functional genes revealed that Clostridiales, particularly Desulfosporosinus (136 bp T-RF) contained bssA genes and were key toluene degraders during methanogenesis dominated by Methanosaeta. Deltaproteobacterial Desulfobulbaceae (157 bp T-RF) became dominant under sulfidogenic conditions, likely because the Desulfosporosinus T-RF 136 apparently lacks dsrB and therefore, unlike its close relatives, is presumed incapable of dissimilatory sulfate reduction. We infer incomplete oxidation of toluene by Desulfosporosinus in syntrophic association with Methanosaeta under methanogenic conditions, and complete toluene oxidation by Desulfobulbaceae during sulfate reduction. © FEMS 2015. All rights reserved. For permissions, please e-mail:

  3. Artificial urushi. (United States)

    Kobayashi, S; Uyama, H; Ikeda, R


    A new concept for the design and laccase-catalyzed preparation of "artificial urushi" from new urushiol analogues is described. The curing proceeded under mild reaction conditions to produce the very hard cross-linked film (artificial urushi) with a high gloss surface. A new cross-linkable polyphenol was synthesized by oxidative polymerization of cardanol, a phenol derivative from cashew-nut-shell liquid, by enzyme-related catalysts. The polyphenol was readily cured to produce the film (also artificial urushi) showing excellent dynamic viscoelasticity.

  4. Artificial intelligence

    CERN Document Server

    Ennals, J R


    Artificial Intelligence: State of the Art Report is a two-part report consisting of the invited papers and the analysis. The editor first gives an introduction to the invited papers before presenting each paper and the analysis, and then concludes with the list of references related to the study. The invited papers explore the various aspects of artificial intelligence. The analysis part assesses the major advances in artificial intelligence and provides a balanced analysis of the state of the art in this field. The Bibliography compiles the most important published material on the subject of

  5. NKLP27: a teleost NK-lysin peptide that modulates immune response, induces degradation of bacterial DNA, and inhibits bacterial and viral infection. (United States)

    Zhang, Min; Li, Mo-fei; Sun, Li


    NK-lysin is an antimicrobial protein produced by cytotoxic T lymphocytes and natural killer cells. In this study, we examined the biological property of a peptide, NKLP27, derived from tongue sole (Cynoglossus semilaevis) NK-lysin. NKLP27 is composed of 27 amino acids and shares little sequence identity with known NK-lysin peptides. NKLP27 possesses bactericidal activity against both Gram-negative and Gram-positive bacteria including common aquaculture pathogens. The bactericidal activity of NKLP27 was dependent on the C-terminal five residues, deletion of which dramatically reduced the activity of NKLP27. During its interaction with the target bacterial cells, NKLP27 destroyed cell membrane integrity, penetrated into the cytoplasm, and induced degradation of genomic DNA. In vivo study showed that administration of tongue sole with NKLP27 before bacterial and viral infection significantly reduced pathogen dissemination and replication in tissues. Further study revealed that fish administered with NKLP27 exhibited significantly upregulated expression of the immune genes including those that are known to be involved in antibacterial and antiviral defense. These results indicate that NKLP27 is a novel antimicrobial against bacterial and viral pathogens, and that the observed effect of NKLP27 on bacterial DNA and host gene expression adds new insights to the action mechanism of fish antimicrobial peptides.

  6. NKLP27: a teleost NK-lysin peptide that modulates immune response, induces degradation of bacterial DNA, and inhibits bacterial and viral infection.

    Directory of Open Access Journals (Sweden)

    Min Zhang

    Full Text Available NK-lysin is an antimicrobial protein produced by cytotoxic T lymphocytes and natural killer cells. In this study, we examined the biological property of a peptide, NKLP27, derived from tongue sole (Cynoglossus semilaevis NK-lysin. NKLP27 is composed of 27 amino acids and shares little sequence identity with known NK-lysin peptides. NKLP27 possesses bactericidal activity against both Gram-negative and Gram-positive bacteria including common aquaculture pathogens. The bactericidal activity of NKLP27 was dependent on the C-terminal five residues, deletion of which dramatically reduced the activity of NKLP27. During its interaction with the target bacterial cells, NKLP27 destroyed cell membrane integrity, penetrated into the cytoplasm, and induced degradation of genomic DNA. In vivo study showed that administration of tongue sole with NKLP27 before bacterial and viral infection significantly reduced pathogen dissemination and replication in tissues. Further study revealed that fish administered with NKLP27 exhibited significantly upregulated expression of the immune genes including those that are known to be involved in antibacterial and antiviral defense. These results indicate that NKLP27 is a novel antimicrobial against bacterial and viral pathogens, and that the observed effect of NKLP27 on bacterial DNA and host gene expression adds new insights to the action mechanism of fish antimicrobial peptides.

  7. DNA damage, lysosomal degradation and Bcl-xL deamidation in doxycycline- and minocycline-induced cell death in the K562 leukemic cell line. (United States)

    Fares, Mona; Abedi-Valugerdi, Manuchehr; Hassan, Moustapha; Potácová, Zuzana


    We investigated mechanisms of cytotoxicity induced by doxycycline (doxy) and minocycline (mino) in the chronic myeloid leukemia K562 cell line. Doxy and mino induced cell death in exposure-dependent manner. While annexin V/propidium iodide staining was consistent with apoptosis, the morphological changes in Giemsa staining were more equivocal. A pancaspase inhibitor Z-VAD-FMK partially reverted cell death morphology, but concurrently completely prevented PARP cleavage. Mitochondrial involvement was detected as dissipation of mitochondrial membrane potential and cytochrome C release. DNA double strand breaks detected with γH2AX antibody and caspase-2 activation were found early after the treatment start, but caspase-3 activation was a late event. Decrement of Bcl-xL protein levels and electrophoretic shift of Bcl-xL molecule were induced by both drugs. Phosphorylation of Bcl-xL at serine 62 was ruled out. Similarly, Bcr/Abl tyrosine kinase levels were decreased. Lysosomal inhibitor chloroquine restored Bcl-xL and Bcr/Abl protein levels and inhibited caspase-3 activation. Thus, the cytotoxicity of doxy and mino in K562 cells is mediated by DNA damage, Bcl-xL deamidation and lysosomal degradation with activation of mitochondrial pathway of apoptosis. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Artificial Reefs (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — An artificial reef is a human-made underwater structure, typically built to promote marine life in areas with a generally featureless bottom, control erosion, block...

  9. Artificial Limbs (United States)

    ... diabetes. They may cause you to need an amputation. Traumatic injuries, including from traffic accidents and military combat Cancer Birth defects If you are missing an arm or leg, an artificial limb can sometimes replace it. The device, which is ...

  10. Natural - synthetic - artificial!

    DEFF Research Database (Denmark)

    Nielsen, Peter E


    The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life.......The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life....

  11. Artificial sweeteners

    DEFF Research Database (Denmark)

    Raben, Anne Birgitte; Richelsen, Bjørn


    Artificial sweeteners can be a helpful tool to reduce energy intake and body weight and thereby risk for diabetes and cardiovascular diseases (CVD). Considering the prevailing diabesity (obesity and diabetes) epidemic, this can, therefore, be an important alternative to natural, calorie......-containing sweeteners. The purpose of this review is to summarize the current evidence on the effect of artificial sweeteners on body weight, appetite, and risk markers for diabetes and CVD in humans....

  12. Artificial Blood

    Directory of Open Access Journals (Sweden)

    Umit Yasar


    Full Text Available The problems and additional cost factor involved in collecting and storing human blood, as well as the pending worldwide shortages are the main driving forces in the development of blood substitutes. Studies on artificial blood basically aim to develop oxygen carrying compounds, produce stem cell-based erythrocyte cells in vitro and, implement the functions and movements of natural hemoglobin molecules found in erythrocyte cells through artificial erythrocyte cells. Consequently, major areas of research in artificial blood studies are haemoglobin-based oxygen carriers, perfluorochemicals, respirocytes and stem cells. Even though these artificial erythrocyte cells do not qualify as perfect red blood cell substitutes yet, they have many potential clinical and non clinical uses. Studies are being carried out on the elimination of side effects of blood substitutes and extensive clinical trials are being conducted to test their safety and efficacy. Artificial blood substitutes could only be used clinically for patient management following clinical trials and approvals, and will be the ultimate global solution to the problems associated with donor scarcity, blood collection and transfusion-mediated diseases. [Archives Medical Review Journal 2012; 21(2.000: 95-108

  13. Low-cost label-free electrical detection of artificial DNA nanostructures using solution-processed oxide thin-film transistors. (United States)

    Kim, Si Joon; Jung, Joohye; Lee, Keun Woo; Yoon, Doo Hyun; Jung, Tae Soo; Dugasani, Sreekantha Reddy; Park, Sung Ha; Kim, Hyun Jae


    A high-sensitivity, label-free method for detecting deoxyribonucleic acid (DNA) using solution-processed oxide thin-film transistors (TFTs) was developed. Double-crossover (DX) DNA nanostructures with different concentrations of divalent Cu ion (Cu(2+)) were immobilized on an In-Ga-Zn-O (IGZO) back-channel surface, which changed the electrical performance of the IGZO TFTs. The detection mechanism of the IGZO TFT-based DNA biosensor is attributed to electron trapping and electrostatic interactions caused by negatively charged phosphate groups on the DNA backbone. Furthermore, Cu(2+) in DX DNA nanostructures generates a current path when a gate bias is applied. The direct effect on the electrical response implies that solution-processed IGZO TFTs could be used to realize low-cost and high-sensitivity DNA biosensors.

  14. Artificial Intelligence

    CERN Document Server

    Warwick, Kevin


    if AI is outside your field, or you know something of the subject and would like to know more then Artificial Intelligence: The Basics is a brilliant primer.' - Nick Smith, Engineering and Technology Magazine November 2011 Artificial Intelligence: The Basics is a concise and cutting-edge introduction to the fast moving world of AI. The author Kevin Warwick, a pioneer in the field, examines issues of what it means to be man or machine and looks at advances in robotics which have blurred the boundaries. Topics covered include: how intelligence can be defined whether machines can 'think' sensory

  15. Preparation of calcium phosphate cement for artificial rib scaffold and its degradability in vivo%人工肋骨支架多孔磷酸钙的制备及体内降解研究

    Institute of Scientific and Technical Information of China (English)

    唐华; 徐志飞; 刘昌胜; 秦雄; 赵学维; 薛磊


    目的 对多孔磷酸钙(CPC)体内降解情况进行研究,为其作为组织工程化人工肋骨支架提供实验基础.方法 将CPC材料埋植于兔皮下,并于预定的时间点将材料取出,称重并送扫描电镜检查,以观察其降解情况;其周围组织则进行苏木素-伊红(HE)染色和透射电镜检查,以观察其炎症反应和生物相容性.结果 CPC材料在术后2、4、8、12、24周的生物吸收率分别为(2.500±0.098)%、(7.000±0.167)%、(10.000±0.242)%、(14.000±0.251)%、(30.000±0.177)%,降解速度平稳,能有效维持缺损部位的稳定性;HE染色和透射电镜结果 显示其炎症反应于4周时消失,有良好的生物相容性.结论 CPC的体内降解速度平稳,组织相容性好,是承重部位和非承重部位的良好组织工程支架.%Objective In order to provide the further evidence of possibiLty of Calcium phosvhate cement(CPC)as the suitable scaffold for tissue engineered artificial rib,the degradation of CPC in vivo was studied.Methods The CPC materials were implanted subcutaneously in rabbits.CPC materials were taken out at the seheduled time points,weighed and examined under a transmission electron microscope.CPC degradation was observed.The tissues around the CPC materials were observed by HE staining and the transmission electron microscope.Results The mass weight loss rate of CPC at 2,4,8,12,24 week was(2.500±0.098)%,(7.000±0.167)%,(10.000±0.242)%,(14.000±0.251)%and (30.000±0.177)% respectively.The speed of degradation was stable.The results of HE staining and transmission electron microscopy revealed that the CPC material had a good compatibility wlth body.Conclusion CPC is a suitable scaffold for tissue engineered artifieial rib.

  16. Artificial intelligence in hematology. (United States)

    Zini, Gina


    Artificial intelligence (AI) is a computer based science which aims to simulate human brain faculties using a computational system. A brief history of this new science goes from the creation of the first artificial neuron in 1943 to the first artificial neural network application to genetic algorithms. The potential for a similar technology in medicine has immediately been identified by scientists and researchers. The possibility to store and process all medical knowledge has made this technology very attractive to assist or even surpass clinicians in reaching a diagnosis. Applications of AI in medicine include devices applied to clinical diagnosis in neurology and cardiopulmonary diseases, as well as the use of expert or knowledge-based systems in routine clinical use for diagnosis, therapeutic management and for prognostic evaluation. Biological applications include genome sequencing or DNA gene expression microarrays, modeling gene networks, analysis and clustering of gene expression data, pattern recognition in DNA and proteins, protein structure prediction. In the field of hematology the first devices based on AI have been applied to the routine laboratory data management. New tools concern the differential diagnosis in specific diseases such as anemias, thalassemias and leukemias, based on neural networks trained with data from peripheral blood analysis. A revolution in cancer diagnosis, including the diagnosis of hematological malignancies, has been the introduction of the first microarray based and bioinformatic approach for molecular diagnosis: a systematic approach based on the monitoring of simultaneous expression of thousands of genes using DNA microarray, independently of previous biological knowledge, analysed using AI devices. Using gene profiling, the traditional diagnostic pathways move from clinical to molecular based diagnostic systems.

  17. Artificial Consciousness or Artificial Intelligence

    Directory of Open Access Journals (Sweden)

    Spanache Florin


    Full Text Available Artificial intelligence is a tool designed by people for the gratification of their own creative ego, so we can not confuse conscience with intelligence and not even intelligence in its human representation with conscience. They are all different concepts and they have different uses. Philosophically, there are differences between autonomous people and automatic artificial intelligence. This is the difference between intelligence and artificial intelligence, autonomous versus automatic. But conscience is above these differences because it is neither conditioned by the self-preservation of autonomy, because a conscience is something that you use to help your neighbor, nor automatic, because one’s conscience is tested by situations which are not similar or subject to routine. So, artificial intelligence is only in science-fiction literature similar to an autonomous conscience-endowed being. In real life, religion with its notions of redemption, sin, expiation, confession and communion will not have any meaning for a machine which cannot make a mistake on its own.

  18. Modeling and time-dependent dynamics of processes of stimulated depolymerization, auto-repairing, degradation and radiation curing of DNA macromolecules and biopolymers at separated and combined actions of ionizing irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Vysotskii, Vladimir I. E-mail:; Pinchuk, Anatoliy O.; Kornilova, Alla A.; Samoylenko, Igor I


    The time-dependent dynamics of the formation, relaxation and auto-repairing of double breaks of DNA macromolecules at the combined radiation action and non-radiation processes of degradation (e.g. by free radicals) were considered. The auto-repairing of DNA double breaks is connected with the peculiarities of long-range interaction of nucleotide charges, atoms and molecules in the intracellular milieu. The properties of intracellular liquid and the characteristics of force interaction between the end-pairs of nucleotides in the area of DNA break in response to radiation are changed. Each kind of radiation is characterized by a certain effectiveness of the double DNA break formation but simultaneously one creates the conditions for their liquidation. On the basis of the analysis and correlation of these processes the time-dependent theory for DNA degradation was created, including hormesis phenomenon, radiation antagonism, the validity of anomaly influence of low and large doses at sharp and chronic radiation and other effects. The qualitative and quantitative correspondences of the theory and experimental results of radiation biology were obtained.

  19. Artificial Intelligence. (United States)

    Lawrence, David R; Palacios-González, César; Harris, John


    It seems natural to think that the same prudential and ethical reasons for mutual respect and tolerance that one has vis-à-vis other human persons would hold toward newly encountered paradigmatic but nonhuman biological persons. One also tends to think that they would have similar reasons for treating we humans as creatures that count morally in our own right. This line of thought transcends biological boundaries-namely, with regard to artificially (super)intelligent persons-but is this a safe assumption? The issue concerns ultimate moral significance: the significance possessed by human persons, persons from other planets, and hypothetical nonorganic persons in the form of artificial intelligence (AI). This article investigates why our possible relations to AI persons could be more complicated than they first might appear, given that they might possess a radically different nature to us, to the point that civilized or peaceful coexistence in a determinate geographical space could be impossible to achieve.

  20. The cAMP signaling system inhibits the repair of {gamma}-ray-induced DNA damage by promoting Epac1-mediated proteasomal degradation of XRCC1 protein in human lung cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Eun-Ah [Department of Biochemistry and Molecular Biology, Cancer Research Center, Seoul National University College of Medicine, Seoul 110-799 (Korea, Republic of); Juhnn, Yong-Sung, E-mail: [Department of Biochemistry and Molecular Biology, Cancer Research Center, Seoul National University College of Medicine, Seoul 110-799 (Korea, Republic of)


    Highlights: Black-Right-Pointing-Pointer cAMP signaling system inhibits repair of {gamma}-ray-induced DNA damage. Black-Right-Pointing-Pointer cAMP signaling system inhibits DNA damage repair by decreasing XRCC1 expression. Black-Right-Pointing-Pointer cAMP signaling system decreases XRCC1 expression by promoting its proteasomal degradation. Black-Right-Pointing-Pointer The promotion of XRCC1 degradation by cAMP signaling system is mediated by Epac1. -- Abstract: Cyclic AMP is involved in the regulation of metabolism, gene expression, cellular growth and proliferation. Recently, the cAMP signaling system was found to modulate DNA-damaging agent-induced apoptosis by regulating the expression of Bcl-2 family proteins and inhibitors of apoptosis. Thus, we hypothesized that the cAMP signaling may modulate DNA repair activity, and we investigated the effects of the cAMP signaling system on {gamma}-ray-induced DNA damage repair in lung cancer cells. Transient expression of a constitutively active mutant of stimulatory G protein (G{alpha}sQL) or treatment with forskolin, an adenylyl cyclase activator, augmented radiation-induced DNA damage and inhibited repair of the damage in H1299 lung cancer cells. Expression of G{alpha}sQL or treatment with forskolin or isoproterenol inhibited the radiation-induced expression of the XRCC1 protein, and exogenous expression of XRCC1 abolished the DNA repair-inhibiting effect of forskolin. Forskolin treatment promoted the ubiquitin and proteasome-dependent degradation of the XRCC1 protein, resulting in a significant decrease in the half-life of the protein after {gamma}-ray irradiation. The effect of forskolin on XRCC1 expression was not inhibited by PKA inhibitor, but 8-pCPT-2 Prime -O-Me-cAMP, an Epac-selective cAMP analog, increased ubiquitination of XRCC1 protein and decreased XRCC1 expression. Knockdown of Epac1 abolished the effect of 8-pCPT-2 Prime -O-Me-cAMP and restored XRCC1 protein level following {gamma}-ray irradiation. From

  1. Artificial blood.



    #Blood substitutes have been developed for almost a century. The various type of artificial blood was continuously available on the market. The theme of this report is to identify the best substitute in emergency situation for some patients and science students. The definition of best is given; thus, as the vital part of the report, the comparison between them is described and discussed. Modified hemoglobin, bovine-based hemoglobin and PFCs are three basic types. In terms of the perfor...

  2. Artificial vision. (United States)

    Zarbin, M; Montemagno, C; Leary, J; Ritch, R


    A number treatment options are emerging for patients with retinal degenerative disease, including gene therapy, trophic factor therapy, visual cycle inhibitors (e.g., for patients with Stargardt disease and allied conditions), and cell transplantation. A radically different approach, which will augment but not replace these options, is termed neural prosthetics ("artificial vision"). Although rewiring of inner retinal circuits and inner retinal neuronal degeneration occur in association with photoreceptor degeneration in retinitis pigmentosa (RP), it is possible to create visually useful percepts by stimulating retinal ganglion cells electrically. This fact has lead to the development of techniques to induce photosensitivity in cells that are not light sensitive normally as well as to the development of the bionic retina. Advances in artificial vision continue at a robust pace. These advances are based on the use of molecular engineering and nanotechnology to render cells light-sensitive, to target ion channels to the appropriate cell type (e.g., bipolar cell) and/or cell region (e.g., dendritic tree vs. soma), and on sophisticated image processing algorithms that take advantage of our knowledge of signal processing in the retina. Combined with advances in gene therapy, pathway-based therapy, and cell-based therapy, "artificial vision" technologies create a powerful armamentarium with which ophthalmologists will be able to treat blindness in patients who have a variety of degenerative retinal diseases.

  3. Sliding Window Analyses for Optimal Selection of Mini-Barcodes, and Application to 454-Pyrosequencing for Specimen Identification from Degraded DNA

    DEFF Research Database (Denmark)

    Boyer, Stephane; Brown, Samuel D J; Collins, Rupert A


    DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI) is over 600 base pairs (bp), amplifi...

  4. Artificial Gravity

    CERN Document Server

    Clément, Gilles


    Protecting the health, safety, and performance of exploration-class mission crews against the physiological deconditioning resulting from long-term weightlessness during transit and long-term reduced gravity during surface operations will require effective, multi-system countermeasures. Artificial gravity, which would replace terrestrial gravity with inertial forces generated by rotating the transit vehicle or by short-radius human centrifuge devices within the transit vehicle or surface habitat, has long been considered a potential solution. However, despite its attractiveness as an efficient

  5. Study on Suitability of KOD DNA Polymerase for Enzymatic Production of Artificial Nucleic Acids Using Base/Sugar Modified Nucleoside Triphosphates

    Directory of Open Access Journals (Sweden)

    Satoshi Obika


    Full Text Available Recently, KOD and its related DNA polymerases have been used for preparing various modified nucleic acids, including not only base-modified nucleic acids, but also sugar-modified ones, such as bridged/locked nucleic acid (BNA/LNA which would be promising candidates for nucleic acid drugs. However, thus far, reasons for the effectiveness of KOD DNA polymerase for such purposes have not been clearly elucidated. Therefore, using mutated KOD DNA polymerases, we studied here their catalytic properties upon enzymatic incorporation of nucleotide analogues with base/sugar modifications. Experimental data indicate that their characteristic kinetic properties enabled incorporation of various modified nucleotides. Among those KOD mutants, one achieved efficient successive incorporation of bridged nucleotides with a 2′-ONHCH2CH2-4′ linkage. In this study, the characteristic kinetic properties of KOD DNA polymerase for modified nucleoside triphosphates were shown, and the effectiveness of genetic engineering in improvement of the enzyme for modified nucleotide polymerization has been demonstrated.

  6. Artificial rheotaxis. (United States)

    Palacci, Jérémie; Sacanna, Stefano; Abramian, Anaïs; Barral, Jérémie; Hanson, Kasey; Grosberg, Alexander Y; Pine, David J; Chaikin, Paul M


    Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes.

  7. CRISPR/Cas9-based generation of knockdown mice by intronic insertion of artificial microRNA using longer single-stranded DNA. (United States)

    Miura, Hiromi; Gurumurthy, Channabasavaiah B; Sato, Takehito; Sato, Masahiro; Ohtsuka, Masato


    Knockdown mouse models, where gene dosages can be modulated, provide valuable insights into gene function. Typically, such models are generated by embryonic stem (ES) cell-based targeted insertion, or pronuclear injection, of the knockdown expression cassette. However, these methods are associated with laborious and time-consuming steps, such as the generation of large constructs with elements needed for expression of a functional RNAi-cassette, ES-cell handling, or screening for mice with the desired knockdown effect. Here, we demonstrate that reliable knockdown models can be generated by targeted insertion of artificial microRNA (amiRNA) sequences into a specific locus in the genome [such as intronic regions of endogenous eukaryotic translation elongation factor 2 (eEF-2) gene] using the Clustered Regularly Interspaced Short Palindromic Repeats/Crispr associated 9 (CRISPR/Cas9) system. We used in vitro synthesized single-stranded DNAs (about 0.5-kb long) that code for amiRNA sequences as repair templates in CRISPR/Cas9 mutagenesis. Using this approach we demonstrate that amiRNA cassettes against exogenous (eGFP) or endogenous [orthodenticle homeobox 2 (Otx2)] genes can be efficiently targeted to a predetermined locus in the genome and result in knockdown of gene expression. We also provide a strategy to establish conditional knockdown models with this method.

  8. The stability and degradation of dietary DNA in the gastrointestinal tract of mammals: implications for horizontal gene transfer and the biosafety of GMOs. (United States)

    Rizzi, Aurora; Raddadi, Noura; Sorlini, Claudia; Nordgrd, Lise; Nielsen, Kaare Magne; Daffonchio, Daniele


    The fate of dietary DNA in the gastrointestinal tract (GIT) of animals has gained renewed interest after the commercial introduction of genetically modified organisms (GMO). Among the concerns regarding GM food, are the possible consequences of horizontal gene transfer (HGT) of recombinant dietary DNA to bacteria or animal cells. The exposure of the GIT to dietary DNA is related to the extent of food processing, food composition, and to the level of intake. Animal feeding studies have demonstrated that a minor amount of fragmented dietary DNA may resist the digestive process. Mammals have been shown to take up dietary DNA from the GIT, but stable integration and expression of internalized DNA has not been demonstrated. Despite the ability of several bacterial species to acquire external DNA by natural transformation, in vivo transfer of dietary DNA to bacteria in the intestine has not been detected in the few experimental studies conducted so far. However, major methodological limitations and knowledge gaps of the mechanistic aspects of HGT calls for methodological improvements and further studies to understand the fate of various types of dietary DNA in the GIT.

  9. Targeted rapid amplification of cDNA ends (T-RACE)—an improved RACE reaction through degradation of non-target sequences


    Neil I Bower; Johnston, Ian A


    Amplification of the 5' ends of cDNA, although simple in theory, can often be difficult to achieve. We describe a novel method for the specific amplification of cDNA ends. An oligo-dT adapter incorporating a dUTP-containing PCR primer primes first-strand cDNA synthesis incorporating dUTP. Using the Cap finder approach, another distinct dUTP containing adapter is added to the 3' end of the newly synthesized cDNA. Second-strand synthesis incorporating dUTP is achieved by PCR, using dUTP-contain...

  10. Artificial Economy

    Directory of Open Access Journals (Sweden)

    Alexandru JIVAN


    Full Text Available This paper proposes to eliminate, a routine in the economic thinking, claimed to be responsible for the negative essence of economic developments, from the point of view, of the ecological implications (employment in the planetary ecosystem. The methodological foundations start from the natural origins of the functionality of the human economic society according to the originary physiocrat liberalism, and from specific natural characteristics of the humankind. This paper begins with a comment-analysis of the difference between natural and artificial within the economy, and then explains some of the most serious diversions from the natural essence of economic liberalism. It shall be explained the original (heterodox interpretation of the Classical political economy (economics, by making calls to the Romanian economic thinking from aggravating past century. Highlighting the destructive impact of the economy - which, under the invoked doctrines, we call unnatural - allows an intuitive presentation of a logical extension of Marshall's market price, based on previous research. Besides the doctrinal arguments presented, the economic realities inventoried along the way (major deficiencies and effects, determined demonstrate the validity of the hypothesis of the unnatural character and therefore necessarily to be corrected, of the concept and of the mechanisms of the current economy.The results of this paper consist of original heterodox methodspresented, intuitive or developed that can be found conclusively within the key proposals for education and regulation.

  11. DNA fragmentation in apoptosis

    Institute of Scientific and Technical Information of China (English)


    Cleavage of chromosomal DNA into oligonucleosomal size fragments is an integral part of apoptosis. Elegant biochemical work identified the DNA fragmentation factor (DFF) as a major apoptotic endonuclease for DNA fragmentation in vitro. Genetic studies in mice support the importance of DFF in DNA fragmentation and possibly in apoptosis in vivo. Recent work also suggests the existence of additional endonucleases for DNA degradation. Understanding the roles of individual endonucleases in apoptosis, and how they might coordinate to degrade DNA in different tissues during normal development and homeostasis, as well as in various diseased states, will be a major research focus in the near future.

  12. Persistence of DNA of Gaeumannomyces graminis var. tritici in soil as measured by a DNA-based assay. (United States)

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


    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

  13. Design and self-assembly of simple coat proteins for artificial viruses. (United States)

    Hernandez-Garcia, Armando; Kraft, Daniela J; Janssen, Anne F J; Bomans, Paul H H; Sommerdijk, Nico A J M; Thies-Weesie, Dominique M E; Favretto, Marco E; Brock, Roland; de Wolf, Frits A; Werten, Marc W T; van der Schoot, Paul; Stuart, Martien Cohen; de Vries, Renko


    Viruses are among the simplest biological systems and are highly effective vehicles for the delivery of genetic material into susceptible host cells. Artificial viruses can be used as model systems for providing insights into natural viruses and can be considered a testing ground for developing artificial life. Moreover, they are used in biomedical and biotechnological applications, such as targeted delivery of nucleic acids for gene therapy and as scaffolds in material science. In a natural setting, survival of viruses requires that a significant fraction of the replicated genomes be completely protected by coat proteins. Complete protection of the genome is ensured by a highly cooperative supramolecular process between the coat proteins and the nucleic acids, which is based on reversible, weak and allosteric interactions only. However, incorporating this type of supramolecular cooperativity into artificial viruses remains challenging. Here, we report a rational design for a self-assembling minimal viral coat protein based on simple polypeptide domains. Our coat protein features precise control over the cooperativity of its self-assembly with single DNA molecules to finally form rod-shaped virus-like particles. We confirm the validity of our design principles by showing that the kinetics of self-assembly of our virus-like particles follows a previous model developed for tobacco mosaic virus. We show that our virus-like particles protect DNA against enzymatic degradation and transfect cells with considerable efficiency, making them promising delivery vehicles.

  14. Interaction of Ddc1 and RPA with single-stranded/double-stranded DNA junctions in yeast whole cell extracts: Proteolytic degradation of the large subunit of replication protein A in ddc1Δ strains. (United States)

    Sukhanova, Maria V; D'Herin, Claudine; Boiteux, Serge; Lavrik, Olga I


    To characterize proteins that interact with single-stranded/double-stranded (ss/ds) DNA junctions in whole cell free extracts of Saccharomyces cerevisiae, we used [(32)P]-labeled photoreactive partial DNA duplexes containing a 3'-ss/ds-junction (3'-junction) or a 5'-ss/ds-junction (5'-junction). Identification of labeled proteins was achieved by MALDI-TOF mass spectrometry peptide mass fingerprinting and genetic analysis. In wild-type extract, one of the components of the Ddc1-Rad17-Mec3 complex, Ddc1, was found to be preferentially photocrosslinked at a 3'-junction. On the other hand, RPAp70, the large subunit of the replication protein A (RPA), was the predominant crosslinking product at a 5'-junction. Interestingly, ddc1Δ extracts did not display photocrosslinking of RPAp70 at a 5'-junction. The results show that RPAp70 crosslinked to DNA with a 5'-junction is subject to limited proteolysis in ddc1Δ extracts, whereas it is stable in WT, rad17Δ, mec3Δ and mec1Δ extracts. The degradation of the RPAp70-DNA adduct in ddc1Δ extract is strongly reduced in the presence of the proteasome inhibitor MG 132. We also addressed the question of the stability of free RPA, using anti-RPA antibodies. The results show that RPAp70 is also subject to proteolysis without photocrosslinking to DNA upon incubation in ddc1Δ extract. The data point to a novel property of Ddc1, modulating the turnover of DNA binding proteins such as RPAp70 by the proteasome.

  15. The flexibility of UV-inducible mutation in Deinococcus ficus as evidenced by the existence of the imuB-dnaE2 gene cassette and generation of superior feather degrading bacteria. (United States)

    Zeng, You-Hong; Shen, Fo-Ting; Tan, Chen-Chung; Huang, Chieh-Chen; Young, Chiu-Chung


    The lexA-imuB-dnaE2 gene cassette contributing to the TLS (translesion synthesis) polymerase activity and can easily cause mutation after DNA damage in many bacteria. But it was previously thought that TLS polymerase activity was unlikely to exist in the radio-resistant genus Deinococcus. In our preliminary studies, the lexA-imuB-dnaE2 gene cassette was found in a newly isolated feather-degrading Deinococcus ficus. Here we have attempted to determine the imuB gene sequence from another Deinococcus species namely D. grandis, by using the newly designed primers. The destroying of either imuB or dnaE2 gene in D. ficus leads to the increase in UV sensitivity and decrease in UV-induced mutations, which demonstrated the existence of TLS polymerase activity in D. ficus. In the presence of lexA-imuB-dnaE2, it is possible to obtain mutants with various keratinolytic activities after UV exposure. The keratinolytic activity of mutant strain CC-ZG207 increased by approximately twofold during growth in liquid feather medium. In contrast, the mutant strain CC-ZG227 showed only half of the keratinolytic activity compared with the wild type strain. By utilizing SDS-PAGE and zymogram profile analysis, the change in the protease activity was observed. We have proposed that the superior mutants of D. ficus can be created under UV stress, which is mediated by the lexA-imuB-dnaE2 gene cassette.

  16. An isothermal primer extension method for whole genome amplification of fresh and degraded DNA: applications in comparative genomic hybridization, genotyping and mutation screening. (United States)

    Lee, Cheryl I P; Leong, Siew Hong; Png, Adrian E H; Choo, Keng Wah; Syn, Christopher; Lim, Dennis T H; Law, Hai Yang; Kon, Oi Lian


    We describe a protocol that uses a bioinformatically optimized primer in an isothermal whole genome amplification (WGA) reaction. Overnight incubation at 37 degrees C efficiently generates several hundred- to several thousand-fold increases in input DNA. The amplified product retains reasonably faithful quantitative representation of unamplified whole genomic DNA (gDNA). We provide protocols for applying this isothermal primer extension WGA protocol in three different techniques of genomic analysis: comparative genomic hybridization (CGH), genotyping at simple tandem repeat (STR) loci and screening for single base mutations in a common monogenic disorder, beta-thalassemia. gDNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues can also be amplified with this protocol.

  17. Transcellular degradation of axonal mitochondria. (United States)

    Davis, Chung-ha O; Kim, Keun-Young; Bushong, Eric A; Mills, Elizabeth A; Boassa, Daniela; Shih, Tiffany; Kinebuchi, Mira; Phan, Sebastien; Zhou, Yi; Bihlmeyer, Nathan A; Nguyen, Judy V; Jin, Yunju; Ellisman, Mark H; Marsh-Armstrong, Nicholas


    It is generally accepted that healthy cells degrade their own mitochondria. Here, we report that retinal ganglion cell axons of WT mice shed mitochondria at the optic nerve head (ONH), and that these mitochondria are internalized and degraded by adjacent astrocytes. EM demonstrates that mitochondria are shed through formation of large protrusions that originate from otherwise healthy axons. A virally introduced tandem fluorophore protein reporter of acidified mitochondria reveals that acidified axonal mitochondria originating from the retinal ganglion cell are associated with lysosomes within columns of astrocytes in the ONH. According to this reporter, a greater proportion of retinal ganglion cell mitochondria are degraded at the ONH than in the ganglion cell soma. Consistently, analyses of degrading DNA reveal extensive mtDNA degradation within the optic nerve astrocytes, some of which comes from retinal ganglion cell axons. Together, these results demonstrate that surprisingly large proportions of retinal ganglion cell axonal mitochondria are normally degraded by the astrocytes of the ONH. This transcellular degradation of mitochondria, or transmitophagy, likely occurs elsewhere in the CNS, because structurally similar accumulations of degrading mitochondria are also found along neurites in superficial layers of the cerebral cortex. Thus, the general assumption that neurons or other cells necessarily degrade their own mitochondria should be reconsidered.

  18. Electroanalytical studies of sulfentrazone in protic medium, its degradation by the electro-Fenton process, and toxicity assessment using ss-DNA. (United States)

    de A Lima, Augusto C; dos S Melo, Acácia M; Pires, Edjane Vieira; dos Santos Ferreira, Roberta Costa; Sant'Ana, Antônio E G; Goulart, Marília O F; de Abreu, Fabiane C


    Sulfentrazone is an herbicide used as a pre-plant incorporated or pre-emergence treatment. The electrochemical oxidation of sulfentrazone was studied, by cyclic, differential and square-wave voltammetry on unmodified and on glassy carbon nanotube-modified electrodes, and by controlled-potential coulometry and electrolysis. The voltammograms of sulfentrazone showed a main irreversible diffusion-controlled pH-dependent oxidation peak. The in situ DNA-damaging capacity of sulfentrazone was also investigated, employing double stranded ds-DNA-modified glassy carbon electrode, without evidence of interaction. On the other hand, in a solution of sulfentrazone and single stranded ss-DNA, the oxidation signals of the respective bases decreased concentration-dependently, indicating binding of sulfentrazone to guanine and adenine. The electro-Fenton method was employed to promote decontamination by eliminating the herbicide, resulting in almost 60% of mineralization.

  19. Degradation products of the artificial azo dye, Allura red, inhibit esterase activity of carbonic anhydrase II: A basic in vitro study on the food safety of the colorant in terms of enzyme inhibition. (United States)

    Esmaeili, Sajjad; Ashrafi-Kooshk, Mohammad Reza; Khaledian, Koestan; Adibi, Hadi; Rouhani, Shohre; Khodarahmi, Reza


    Allura red is a widely used food colorant, but there is debate on its potential security risk. In the present study, we found that degradation products of the dye were more potent agents with higher carbonic anhydrase inhibitory action than the parent dye. The mechanism by which the compounds inhibit the enzyme activity has been determined as competitive mode. In addition, the enzyme binding properties of the compounds were investigated employing different spectroscopic techniques and molecular docking. The analyses of fluorescence quenching data revealed the existence of the same binding site for the compounds on the enzyme molecule. The thermodynamic parameters of ligand binding were not similar, which indicates that different interactions are responsible in binding of the parent dye and degradation products to the enzyme. It appears that enzyme inhibition should be considered, more seriously, as a new opened dimension in food safety.

  20. Degradation of fungal DNA in formalin-fixed paraffin-embedded sinus fungal balls hampers reliable sequence-based identification of fungi. (United States)

    Cabaret, Odile; Toussain, Guillaume; Abermil, Nassera; Alsamad, Issam Abd; Botterel, Françoise; Costa, Jean-Marc; Papon, Jean-François; Bretagne, Stéphane


    Identification of the etiologic agent responsible for sinus fungal ball (SFB) is rarely obtained due to either the culture of patient specimens not being ordered or if cultures were inoculated they proved to be negative. Obviously, this has a significant impact on the design of appropriate therapeutic strategies. We investigated whether paraffin-embedded (PE) tissues, the only materials often available, were suitable for the correct identification of the responsible fungi. We obtained PE tissues of SFB from 16 different patients who had risk factors for invasive fungal infections. DNA was extracted using an automated extractor and the internal transcribed spacer (ITS) sequenced following amplification with two sets of primers designed to amplify >300 bp fragments. This was attempted in parallel with a real-time quantitative PCR assay targeting Aspergillus spp. mitochondrial DNA designed to amplify <150 bp fragments. ITS sequencing succeeded in appropriately identifying the etiologic agents in 10 of the 16 samples (nine Aspergillus fumigatus, one Lewia spp.). In contrast, the <150 bp PCR assay amplified all specimens correctly except the one involving Lewia spp. If fungal identification is warranted to understand the pathophysiology of SFB and guide clinicians, we cannot rely only on ITS sequencing of the DNA obtained from PE tissues. The main reason is probably due to the fact that formalin prevents amplification of long DNA fragments and consequently, frozen or fresh tissues should be employed.

  1. A Regulatory Loop Composed of RAP80-HDM2-p53 Provides RAP80-enhanced p53 Degradation by HDM2 in Response to DNA Damage* (United States)

    Yan, Jun; Menendez, Daniel; Yang, Xiao-Ping; Resnick, Michael A.; Jetten, Anton M.


    The ubiquitin interaction motif-containing protein RAP80 plays a key role in DNA damage response signaling. Using genomic and functional analysis, we established that the expression of the RAP80 gene is regulated in a DNA damage-responsive manner by the master regulator p53. This regulation occurs at the transcriptional level through a noncanonical p53 response element in the RAP80 promoter. Although it is inducible by p53, RAP80 is also able to regulate p53 through an association with both p53 and the E3 ubiquitin ligase HDM2, providing HDM2-dependent enhancement of p53 polyubiquitination. Depletion of RAP80 by small interfering RNA stabilizes p53, which, following DNA damage, results in an increased transactivation of several p53 target genes as well as greater apoptosis. Consistent with these observations, exogenous expression of RAP80 selectively inhibits p53-dependent transactivation of target genes in an mdm2-dependent manner in MEF cells. Thus, we identify a new DNA damage-associated role for RAP80. It can function in an autoregulatory loop consisting of RAP80, HDM2, and the p53 master regulatory network, implying an important role for this loop in genome stability and oncogenesis. PMID:19433585

  2. Trends in Artificial Intelligence. (United States)

    Hayes, Patrick


    Discusses the foundations of artificial intelligence as a science and the types of answers that may be given to the question, "What is intelligence?" The paradigms of artificial intelligence and general systems theory are compared. (Author/VT)

  3. New insights into estrogenic regulation of O(6)-methylguanine DNA-methyltransferase (MGMT) in human breast cancer cells: Co-degradation of ER-α and MGMT proteins by fulvestrant or O(6)-benzylguanine indicates fresh avenues for therapy. (United States)

    Paranjpe, Ameya; Bailey, Nathan I; Konduri, Santhi; Bobustuc, George C; Ali-Osman, Francis; Yusuf, Mohd A; Punganuru, Surendra R; Madala, Hanumantha Rao; Basak, Debasish; Mostofa, Agm; Srivenugopal, Kalkunte S


    Endocrine therapy using estrogen receptor-α (ER-α) antagonists for attenuating horm2one-driven cell proliferation is a major treatment modality for breast cancers. To exploit any DNA repair deficiencies associated with endocrine therapy, we investigated the functional and physical interactions of ER-α with O(6)-methylguanine DNA methyltransferase (MGMT), a unique DNA repair protein that confers tumor resistance to various anticancer alkylating agents. The ER-α -positive breast cancer cell lines (MCF-7, T47D) and ER- negative cell lines (MDAMB-468, MDAMB-231), and established inhibitors of ER-α and MGMT, namely, ICI-182,780 (Faslodex) and O(6)-benzylguanine, respectively, were used to study MGMT- ER interactions. The MGMT gene promoter was found to harbor one full and two half estrogen-responsive elements (EREs) and two antioxidant-responsive elements (AREs). MGMT expression was upregulated by estrogen, downregulated by tamoxifen in Western blot and promoter-linked reporter assays. Similarly, both transient and stable transfections of Nrf-2 (nuclear factor-erythroid 2-related factor-2) increased the levels of MGMT protein and activity 3 to 4-fold reflecting novel regulatory nodes for this drug-resistance determinant. Of the different ER-α antagonists tested, the pure anti-estrogen fulvestrant was most potent in inhibiting the MGMT activity in a dose, time and ER-α dependent manner, similar to O(6)-benzylguanine. Interestingly, fulvestrant exposure led to a degradation of both ER-α and MGMT proteins and O(6)-benzylguanine also induced a specific loss of ER-α and MGMT proteins in MCF-7 and T47D breast cancer cells with similar kinetics. Immunoprecipitation revealed a specific association of ER-α and MGMT proteins in breast cancer cells. Furthermore, silencing of MGMT gene expression triggered a decrease in the levels of both MGMT and ER-α proteins. The involvement of proteasome in the drug-induced degradation of both proteins was also demonstrated

  4. New insights into estrogenic regulation of O6-methylguanine DNA-methyltransferase (MGMT) in human breast cancer cells: Co-degradation of ER-α and MGMT proteins by fulvestrant or O6-benzylguanine indicates fresh avenues for therapy (United States)

    Paranjpe, Ameya; Bailey, Nathan I.; Konduri, Santhi; Bobustuc, George C.; Ali-Osman, Francis; Yusuf, Mohd. A.; Punganuru, Surendra R.; Madala, Hanumantha Rao; Basak, Debasish; Mostofa, AGM; Srivenugopal, Kalkunte S.


    Abstract Endocrine therapy using estrogen receptor-α (ER-α) antagonists for attenuating horm2one-driven cell proliferation is a major treatment modality for breast cancers. To exploit any DNA repair deficiencies associated with endocrine therapy, we investigated the functional and physical interactions of ER-α with O6-methylguanine DNA methyltransferase (MGMT), a unique DNA repair protein that confers tumor resistance to various anticancer alkylating agents. The ER-α -positive breast cancer cell lines (MCF-7, T47D) and ER- negative cell lines (MDAMB-468, MDAMB-231), and established inhibitors of ER-α and MGMT, namely, ICI-182,780 (Faslodex) and O6-benzylguanine, respectively, were used to study MGMT- ER interactions. The MGMT gene promoter was found to harbor one full and two half estrogen-responsive elements (EREs) and two antioxidant-responsive elements (AREs). MGMT expression was upregulated by estrogen, downregulated by tamoxifen in Western blot and promoter-linked reporter assays. Similarly, both transient and stable transfections of Nrf-2 (nuclear factor-erythroid 2-related factor-2) increased the levels of MGMT protein and activity 3 to 4-fold reflecting novel regulatory nodes for this drug-resistance determinant. Of the different ER-α antagonists tested, the pure anti-estrogen fulvestrant was most potent in inhibiting the MGMT activity in a dose, time and ER-α dependent manner, similar to O6-benzylguanine. Interestingly, fulvestrant exposure led to a degradation of both ER-α and MGMT proteins and O6-benzylguanine also induced a specific loss of ER-α and MGMT proteins in MCF-7 and T47D breast cancer cells with similar kinetics. Immunoprecipitation revealed a specific association of ER-α and MGMT proteins in breast cancer cells. Furthermore, silencing of MGMT gene expression triggered a decrease in the levels of both MGMT and ER-α proteins. The involvement of proteasome in the drug-induced degradation of both proteins was also demonstrated

  5. Artificial life and Piaget. (United States)

    Mueller, Ulrich; Grobman, K H.


    Artificial life provides important theoretical and methodological tools for the investigation of Piaget's developmental theory. This new method uses artificial neural networks to simulate living phenomena in a computer. A recent study by Parisi and Schlesinger suggests that artificial life might reinvigorate the Piagetian framework. We contrast artificial life with traditional cognitivist approaches, discuss the role of innateness in development, and examine the relation between physiological and psychological explanations of intelligent behaviour.

  6. Artificiality in Social Sciences


    Rennard, Jean-Philippe


    This text provides with an introduction to the modern approach of artificiality and simulation in social sciences. It presents the relationship between complexity and artificiality, before introducing the field of artificial societies which greatly benefited from the computer power fast increase, gifting social sciences with formalization and experimentation tools previously owned by "hard" sciences alone. It shows that as "a new way of doing social sciences", artificial societies should undo...

  7. The cDNA 385C to A missense polymorphism of the endocannabinoid degrading enzyme fatty acid amide hydrolase (FAAH) is associated with overweight/obesity but not with binge eating disorder in overweight/obese women. (United States)

    Monteleone, Palmiero; Tortorella, Alfonso; Martiadis, Vassilis; Di Filippo, Carmela; Canestrelli, Benedetta; Maj, Mario


    Endocannabinoids are involved in the modulation of eating behavior; hence, alterations of this system may play a role in obesity. Recently, a single nucleotide polymorphism (cDNA 385C to A) of the gene coding for fatty acid amide hydrolase (FAAH), the major degrading enzyme of endocannabinoids, has been found to be associated with obesity. However, the possibility that the FAAH gene cDNA 385C to A single nucleotide polymorphism (SNP) is associated to binge eating disorder (BED), a condition that frequently occurs in obese individuals, has not been investigated. In order to address this issue, we assessed the distribution of the cDNA 385C to A SNP in 115 overweight/obese subjects with BED, 74 non-BED patients with obesity and 110 normal weight healthy controls. As compared to healthy controls, the whole group of overweight/obese BED and non-BED patients had a significantly higher frequency of the CA genotype and the A allele of the FAAH gene cDNA 385C to A SNP. Moreover, the SNP resulted significantly correlated to the presence of overweight/obesity (F(2, 296)=3.58, P=0.02), but not to the occurrence of BED (F(2, 296)=0.98; P=0.3). The present study confirms previously published significant over-representations of the FAAH 385 A allele in overweight/obese subjects and presents new data in BED patients that the 385 mutation is not significantly associated with BED-related obesity.

  8. An artificial cell based on gene expression in vesicle (United States)

    Noireaux, Vincent


    A new experimental approach is presented to build an artificial cell using the translation machinery of a cell-free expression system as the hardware and a DNA synthetic program as the software. Cytoplasmic extracts, encapsulated in phospholipid vesicles, are used to assemble custom-made genetic circuits to develop the functions of a minimal cell. The objective is to understand how a DNA algorithm can be designed to build an operating system that has some of the properties of life. We show how a long-lived bioreactor is built to carry out in vitro transcription and translation in cell-sized vesicles. To develop the synthetic membrane into an active interface, a few amphipathic peptides and an insertion mechanism of integral membrane proteins have been tested. With vesicles composed of different phospholipids, the fusion protein alpha-hemolysin-eGFP can be expressed to reveal patterns on the membrane. Finally, specific degradation mechanisms are introduced to create a sink for the synthesized messengers and proteins. Perspectives and limitations of this approach will be discussed.

  9. CUPRAC colorimetric and electroanalytical methods determining antioxidant activity based on prevention of oxidative DNA damage. (United States)

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


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

  10. Teaching artificial intelligence to read electropherograms. (United States)

    Taylor, Duncan; Powers, David


    Electropherograms are produced in great numbers in forensic DNA laboratories as part of everyday criminal casework. Before the results of these electropherograms can be used they must be scrutinised by analysts to determine what the identified data tells us about the underlying DNA sequences and what is purely an artefact of the DNA profiling process. A technique that lends itself well to such a task of classification in the face of vast amounts of data is the use of artificial neural networks. These networks, inspired by the workings of the human brain, have been increasingly successful in analysing large datasets, performing medical diagnoses, identifying handwriting, playing games, or recognising images. In this work we demonstrate the use of an artificial neural network which we train to 'read' electropherograms and show that it can generalise to unseen profiles. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  11. Degradation process of lead chromate in paintings by Vincent van Gogh studied by means of spectromicroscopic methods. 4. Artificial aging of model samples of co-precipitates of lead chromate and lead sulfate. (United States)

    Monico, Letizia; Janssens, Koen; Miliani, Costanza; Van der Snickt, Geert; Brunetti, Brunetto Giovanni; Cestelli Guidi, Mariangela; Radepont, Marie; Cotte, Marine


    Previous investigations about the darkening of chrome yellow pigments revealed that this form of alteration is attributable to a reduction of the original Cr(VI) to Cr(III), and that the presence of sulfur-containing compounds, most often sulfates, plays a key role during this process. We recently demonstrated that different crystal forms of chrome yellow pigments (PbCrO(4) and PbCr(1-x)S(x)O(4)) are present in paintings by Vincent van Gogh. In the present work, we show how both the chemical composition and the crystalline structure of lead chromate-based pigments influence their stability. For this purpose, oil model samples made with in-house synthesized powders of PbCrO(4) and PbCr(1-x)S(x)O(4) were artificially aged and characterized. We observed a profound darkening only for those paint models made with PbCr(1-x)S(x)O(4), rich in SO(4)(2-) (x ≥ 0.4), and orthorhombic phases (>30 wt %). Cr and S K-edge micro X-ray absorption near edge structure investigations revealed in an unequivocal manner the formation of up to about 60% of Cr(III)-species in the outer layer of the most altered samples; conversely, independent of the paint models' chemical composition, no change in the S-oxidation state was observed. Analyses employing UV-visible diffuse reflectance and Fourier transform infrared spectroscopy were performed on unaged and aged model samples in order to obtain additional information on the physicochemical changes induced by the aging treatment.

  12. Artificial cognition architectures

    CERN Document Server

    Crowder, James A; Friess, Shelli A


    The goal of this book is to establish the foundation, principles, theory, and concepts that are the backbone of real, autonomous Artificial Intelligence. Presented here are some basic human intelligence concepts framed for Artificial Intelligence systems. These include concepts like Metacognition and Metamemory, along with architectural constructs for Artificial Intelligence versions of human brain functions like the prefrontal cortex. Also presented are possible hardware and software architectures that lend themselves to learning, reasoning, and self-evolution

  13. Artificial life and life artificialization in Tron

    Directory of Open Access Journals (Sweden)

    Carolina Dantas Figueiredo


    Full Text Available Cinema constantly shows the struggle between the men and artificial intelligences. Fiction, and more specifically fiction films, lends itself to explore possibilities asking “what if?”. “What if”, in this case, is related to the eventual rebellion of artificial intelligences, theme explored in the movies Tron (1982 and Tron Legacy (2010 trat portray the conflict between programs and users. The present paper examines these films, observing particularly the possibility programs empowering. Finally, is briefly mentioned the concept of cyborg as a possibility of response to human concerns.

  14. Utilização de redes neurais artificiais na classificação de níveis de degradação em pastagens Use of artificial neural networks in the classification of degradation levels of pastures

    Directory of Open Access Journals (Sweden)

    César S. Chagas


    Full Text Available Este trabalho teve por objetivo avaliar a eficiência dos classificadores redes neurais artificiais (RNA e o de máxima verossimilhança (Maxver na classificação do uso da terra no município de Viçosa, MG, a partir de imagens do sensor ASTER, com ênfase nos níveis de degradação das pastagens. Neste estudo, foram identificados três níveis de degradação das pastagens (moderado, forte e muito forte e avaliada uma composição da imagem do sensor ASTER contendo as 3 bandas do visível e infravermelho próximo, com resolução espacial de 15 m. O simulador de redes neurais empregado foi o "Java Neural Network Simulator" e o algoritmo de aprendizado, o backpropagation. Os resultados mostram que a classificação por redes neurais, embora apresente resultado ligeiramente superior, teve desempenho estatisticamente semelhante ao obtido pela classificação pelo Maxver, obtendo um índice Kappa de 0,80, contra 0,79, respectivamente. Nas classificações realizadas a classe que apresentou maior erro de classificação foi a pastagem no nível de degradação forte, enquanto a maior exatidão na classificação foi obtida pelo café, para ambos os classificadores, com 100 e 96%, respectivamente.The aim of this work is to evaluate the artificial neural networks and the maximum likelihood classification performances to classify land uses at Viçosa, Minas Gerais State, using ASTER images in order to verify degradation levels of pastures. In this study, three different levels of pasture degradation have been identified (moderate, strong and very strong and an image composition of 3 bands was tested (covering the visible and the near infra-red with 15 m of spatial resolution. The neural networks simulator used was the "Neural Java Network Simulator", with a feed forward model and the learning algorithm of back propagation. The obtained results show that the classification using neural networks, while presenting a slightly superior result, had a

  15. Onion artificial muscles (United States)

    Chen, Chien-Chun; Shih, Wen-Pin; Chang, Pei-Zen; Lai, Hsi-Mei; Chang, Shing-Yun; Huang, Pin-Chun; Jeng, Huai-An


    Artificial muscles are soft actuators with the capability of either bending or contraction/elongation subjected to external stimulation. However, there are currently no artificial muscles that can accomplish these actions simultaneously. We found that the single layered, latticed microstructure of onion epidermal cells after acid treatment became elastic and could simultaneously stretch and bend when an electric field was applied. By modulating the magnitude of the voltage, the artificial muscle made of onion epidermal cells would deflect in opposing directions while either contracting or elongating. At voltages of 0-50 V, the artificial muscle elongated and had a maximum deflection of -30 μm; at voltages of 50-1000 V, the artificial muscle contracted and deflected 1.0 mm. The maximum force response is 20 μN at 1000 V.

  16. Transcripts of pectin-degrading enzymes and isolation of complete cDNA sequence of a pectate lyase gene induced by coffee white stem borer (Xylotrechus quadripes) in the bark tissue of Coffea canephora (robusta coffee). (United States)

    Bharathi, Kosaraju; Santosh, P; Sreenath, H L


    Of the two commercially cultivated coffee (Coffea) species, C. arabica (arabica) is highly susceptible and C. canephora (robusta) is highly resistant to the insect pest Xylotrechus quadripes (Coleoptera: Cerambycidae), commonly known as coffee white stem borer (CWSB). We constructed a forward-subtracted cDNA library by Suppression Subtractive Hybridization (SSH) from robusta bark tissue for profiling genes induced by CWSB infestation. Among the 265 unigenes of the SSH EST library, 7 unigenes (5 contigs and 2 singletons) matching different pectin-degrading enzymes were discovered. These ESTs matched one pectate lyase, three polygalacturonases, and one pectin acetylesterase gene. Quantitative real-time PCR (qRT-PCR) revealed that CWSB infestation strongly induces the pectate lyase gene at 72 h. Complete cDNA sequence of the pectate lyase gene was obtained through 3' and 5' RACE reactions. It was a 1595 bp long sequence that included full CDS and both UTRs. Against C. canephora genome sequences in Coffee Genome Hub database ( ), it had 22 matches to different pectate lyase genes mapped on 9 of the 11 pseudochromosomes, the top match being Cc07_g00190 Pectate lyase. In NCBI database, it matched pectate lyase sequences of several plants. Apart from C. canephora, the closest pectate lyase matches were from Sesamum indicum and Nicotiana tabacum. The pectinolytic enzymes discovered here are thought to play a role in the production of oligogalacturonides (OGs) which act as Damage-Associated Molecular Pattern (DAMP) signals eliciting innate immunity in plants. The pectate lyase gene, induced by CWSB infestation, along with other endogenous pectinolytic enzymes and CWSB-specific elicitors, may be involved in triggering basal defense responses to protect the CWSB-damaged tissue against pathogens, as well as to contain CWSB in robusta.

  17. Bacterial isolates degrading aliphatic polycarbonates. (United States)

    Suyama, T; Hosoya, H; Tokiwa, Y


    Bacteria that degrade an aliphatic polycarbonate, poly(hexamethylene carbonate), were isolated from river water in Ibaraki. Prefecture, Japan, after enrichment in liquid medium containing poly(hexamethylene carbonate) suspensions as carbon source, and dilution to single cells. Four of the strains, 35L, WFF52, 61A and 61B2, degraded poly(hexamethylene carbonate) on agar plate containing suspended poly(hexamethylene carbonate). Degradation of poly(hexamethylene carbonate) was confirmed by gel permeation chromatography. Besides poly(hexamethylene carbonate), the strains were found to degrade poly(tetramethylene carbonate). The strains were characterized morphologically, physiologically, and by 16S rDNA sequence analysis. Strains 35L and WFF52 were tentatively identified as Pseudomonas sp. and Variovorax sp., respectively, while strains 61A and 61B2 constitute an unidentified branch within the beta subclass of the Proteobacteria.

  18. The pancreatic and duodenal homeobox protein PDX-1 regulates the ductal specific keratin 19 through the degradation of MEIS1 and DNA binding.

    Directory of Open Access Journals (Sweden)

    Johannes von Burstin

    Full Text Available BACKGROUND: Pancreas organogenesis is the result of well-orchestrated and balanced activities of transcription factors. The homeobox transcription factor PDX-1 plays a crucial role in the development and function of the pancreas, both in the maintenance of progenitor cells and in determination and maintenance of differentiated endocrine cells. However, the activity of homeobox transcription factors requires coordination with co-factors, such as PBX and MEIS proteins. PBX and MEIS proteins belong to the family of three amino acid loop extension (TALE homeodomain proteins. In a previous study we found that PDX-1 negatively regulates the transcriptional activity of the ductal specific keratin 19 (Krt19. In this study, we investigate the role of different domains of PDX-1 and elucidate the functional interplay of PDX-1 and MEIS1 necessary for Krt19 regulation. METHODOLOGY/PRINCIPAL FINDINGS: Here, we demonstrate that PDX-1 exerts a dual manner of regulation of Krt19 transcriptional activity. Deletion studies highlight that the NH(2-terminus of PDX-1 is functionally relevant for the down-regulation of Krt19, as it is required for DNA binding of PDX-1 to the Krt19 promoter. Moreover, this effect occurs independently of PBX. Second, we provide insight on how PDX-1 regulates the Hox co-factor MEIS1 post-transcriptionally. We find specific binding of MEIS1 and MEIS2 to the Krt19 promoter using IP-EMSA, and siRNA mediated silencing of Meis1, but not Meis2, reduces transcriptional activation of Krt19 in primary pancreatic ductal cells. Over-expression of PDX-1 leads to a decreased level of MEIS1 protein, and this decrease is prevented by inhibition of the proteasome. CONCLUSIONS/SIGNIFICANCE: Taken together, our data provide evidence for a dual mechanism of how PDX-1 negatively regulates Krt19 ductal specific gene expression. These findings imply that transcription factors may efficiently regulate target gene expression through diverse, non

  19. Artificial intelligence in medicine. (United States)

    Ramesh, A. N.; Kambhampati, C.; Monson, J. R. T.; Drew, P. J.


    INTRODUCTION: Artificial intelligence is a branch of computer science capable of analysing complex medical data. Their potential to exploit meaningful relationship with in a data set can be used in the diagnosis, treatment and predicting outcome in many clinical scenarios. METHODS: Medline and internet searches were carried out using the keywords 'artificial intelligence' and 'neural networks (computer)'. Further references were obtained by cross-referencing from key articles. An overview of different artificial intelligent techniques is presented in this paper along with the review of important clinical applications. RESULTS: The proficiency of artificial intelligent techniques has been explored in almost every field of medicine. Artificial neural network was the most commonly used analytical tool whilst other artificial intelligent techniques such as fuzzy expert systems, evolutionary computation and hybrid intelligent systems have all been used in different clinical settings. DISCUSSION: Artificial intelligence techniques have the potential to be applied in almost every field of medicine. There is need for further clinical trials which are appropriately designed before these emergent techniques find application in the real clinical setting. PMID:15333167

  20. Polysaccharide Degradation (United States)

    Stone, Bruce A.; Svensson, Birte; Collins, Michelle E.; Rastall, Robert A.

    An overview of current and potential enzymes used to degrade polysaccharides is presented. Such depolymerases are comprised of glycoside hydrolases, glycosyl transferases, phosphorylases and lyases, and their classification, active sites and action patterns are discussed. Additionally, the mechanisms that these enzymes use to cleave glycosidic linkages is reviewed as are inhibitors of depolymerase activity; reagents which react with amino acid residues, glycoside derivatives, transition state inhibitors and proteinaceous inhibitors. The characterization of various enzymes of microbial, animal or plant origin has led to their widespread use in the production of important oligosaccharides which can be incorporated into food stuffs. Sources of polysaccharides of particular interest in this chapter are those from plants and include inulin, dextran, xylan and pectin, as their hydrolysis products are purported to be functional foods in the context of gastrointestinal health. An alternative use of degraded polysaccharides is in the treatment of disease. The possibility exists to treat bacterial exopolysaccharide with lyases from bacteriophage to produce oligosaccharides exhibiting bioactive sequences. Although this area is currently in its infancy the knowledge is available to investigate further.

  1. Collective helicity switching of a DNA-coat assembly (United States)

    Kim, Yongju; Li, Huichang; He, Ying; Chen, Xi; Ma, Xiaoteng; Lee, Myongsoo


    Hierarchical assemblies of biomolecular subunits can carry out versatile tasks at the cellular level with remarkable spatial and temporal precision. As an example, the collective motion and mutual cooperation between complex protein machines mediate essential functions for life, such as replication, synthesis, degradation, repair and transport. Nucleic acid molecules are far less dynamic than proteins and need to bind to specific proteins to form hierarchical structures. The simplest example of these nucleic acid-based structures is provided by a rod-shaped tobacco mosaic virus, which consists of genetic material surrounded by coat proteins. Inspired by the complexity and hierarchical assembly of viruses, a great deal of effort has been devoted to design similarly constructed artificial viruses. However, such a wrapping approach makes nucleic acid dynamics insensitive to environmental changes. This limitation generally restricts, for example, the amplification of the conformational dynamics between the right-handed B form to the left-handed Z form of double-stranded deoxyribonucleic acid (DNA). Here we report a virus-like hierarchical assembly in which the native DNA and a synthetic coat undergo repeated collective helicity switching triggered by pH change under physiological conditions. We also show that this collective helicity inversion occurs during translocation of the DNA-coat assembly into intracellular compartments. Translating DNA conformational dynamics into a higher level of hierarchical dynamics may provide an approach to create DNA-based nanomachines.

  2. Introduction to artificial intelligence (United States)

    Cheeseman, P.; Gevarter, W.


    This paper presents an introductory view of Artificial Intelligence (AI). In addition to defining AI, it discusses the foundations on which it rests, research in the field, and current and potential applications.

  3. Artificial Neural Networks


    Chung-Ming Kuan


    Artificial neural networks (ANNs) constitute a class of flexible nonlinear models designed to mimic biological neural systems. In this entry, we introduce ANN using familiar econometric terminology and provide an overview of ANN modeling approach and its implementation methods.

  4. Artificial Sweeteners in a Large Canadian River Reflect Human Consumption in the Watershed


    John Spoelstra; Sherry L Schiff; Brown, Susan J.


    Artificial sweeteners have been widely incorporated in human food products for aid in weight loss regimes, dental health protection and dietary control of diabetes. Some of these widely used compounds can pass non-degraded through wastewater treatment systems and are subsequently discharged to groundwater and surface waters. Measurements of artificial sweeteners in rivers used for drinking water production are scarce. In order to determine the riverine concentrations of artificial sweeteners ...

  5. Intelligence: Real or artificial?


    Schlinger, Henry D


    Throughout the history of the artificial intelligence movement, researchers have strived to create computers that could simulate general human intelligence. This paper argues that workers in artificial intelligence have failed to achieve this goal because they adopted the wrong model of human behavior and intelligence, namely a cognitive essentialist model with origins in the traditional philosophies of natural intelligence. An analysis of the word “intelligence” suggests that it originally r...

  6. Principles of artificial intelligence

    CERN Document Server

    Nilsson, Nils J


    A classic introduction to artificial intelligence intended to bridge the gap between theory and practice, Principles of Artificial Intelligence describes fundamental AI ideas that underlie applications such as natural language processing, automatic programming, robotics, machine vision, automatic theorem proving, and intelligent data retrieval. Rather than focusing on the subject matter of the applications, the book is organized around general computational concepts involving the kinds of data structures used, the types of operations performed on the data structures, and the properties of th

  7. Physics of Artificial Gravity (United States)

    Bukley, Angie; Paloski, William; Clement, Gilles


    This chapter discusses potential technologies for achieving artificial gravity in a space vehicle. We begin with a series of definitions and a general description of the rotational dynamics behind the forces ultimately exerted on the human body during centrifugation, such as gravity level, gravity gradient, and Coriolis force. Human factors considerations and comfort limits associated with a rotating environment are then discussed. Finally, engineering options for designing space vehicles with artificial gravity are presented.

  8. The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico coastal microbial communities after the Deepwater Horizon oil spill

    Directory of Open Access Journals (Sweden)

    Anthony D. Kappell


    Full Text Available The Deepwater Horizon (DWH blowout resulted in oil transport, including polycyclic aromatic hydrocarbons (PAHs to the Gulf of Mexico shoreline. The microbial communities of these shorelines are thought to be responsible for the intrinsic degradation of PAHs. To investigate the Gulf Coast beach microbial community response to hydrocarbon exposure, we examined the functional gene diversity, bacterial community composition, and PAH degradation capacity of a heavily oiled and non-oiled beach following the oil exposure. With a non-expression functional gene microarray targeting 539 gene families, we detected 28,748 coding sequences. Of these sequences, 10% were uniquely associated with the severely oil-contaminated beach and 6.0% with the non-oiled beach. There was little variation in the functional genes detected between the two beaches; however the relative abundance of functional genes involved in oil degradation pathways, including PAHs, were greater in the oiled beach. The microbial PAH degradation potentials of both beaches, were tested in mesocosms. Mesocosms were constructed in glass columns using sands with native microbial communities, circulated with artificial sea water and challenged with a mixture of PAHs. The low-molecular weight PAHs, fluorene and naphthalene, showed rapid depletion in all mesocosms while the high-molecular weight benzo[α]pyrene was not degraded by either microbial community. Both the heavily oiled and the non-impacted coastal communities showed little variation in their biodegradation ability for low molecular weight PAHs. Massively-parallel sequencing of 16S rRNA genes from mesocosm DNA showed that known PAH degraders and genera frequently associated with oil hydrocarbon degradation represented a major portion of the bacterial community. The observed similar response by microbial communities from beaches with a different recent history of oil exposure suggests that Gulf Coast beach communities are primed for PAH

  9. The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill. (United States)

    Kappell, Anthony D; Wei, Yin; Newton, Ryan J; Van Nostrand, Joy D; Zhou, Jizhong; McLellan, Sandra L; Hristova, Krassimira R


    The Deepwater Horizon (DWH) blowout resulted in oil transport, including polycyclic aromatic hydrocarbons (PAHs) to the Gulf of Mexico shoreline. The microbial communities of these shorelines are thought to be responsible for the intrinsic degradation of PAHs. To investigate the Gulf Coast beach microbial community response to hydrocarbon exposure, we examined the functional gene diversity, bacterial community composition, and PAH degradation capacity of a heavily oiled and non-oiled beach following the oil exposure. With a non-expression functional gene microarray targeting 539 gene families, we detected 28,748 coding sequences. Of these sequences, 10% were uniquely associated with the severely oil-contaminated beach and 6.0% with the non-oiled beach. There was little variation in the functional genes detected between the two beaches; however the relative abundance of functional genes involved in oil degradation pathways, including polycyclic aromatic hydrocarbons (PAHs), were greater in the oiled beach. The microbial PAH degradation potentials of both beaches, were tested in mesocosms. Mesocosms were constructed in glass columns using sands with native microbial communities, circulated with artificial sea water and challenged with a mixture of PAHs. The low-molecular weight PAHs, fluorene and naphthalene, showed rapid depletion in all mesocosms while the high-molecular weight benzo[α]pyrene was not degraded by either microbial community. Both the heavily oiled and the non-impacted coastal communities showed little variation in their biodegradation ability for low molecular weight PAHs. Massively-parallel sequencing of 16S rRNA genes from mesocosm DNA showed that known PAH degraders and genera frequently associated with oil hydrocarbon degradation represented a major portion of the bacterial community. The observed similar response by microbial communities from beaches with a different recent history of oil exposure suggests that Gulf Coast beach communities are

  10. Transcription, reverse transcription, and analysis of RNA containing artificial genetic components. (United States)

    Leal, Nicole A; Kim, Hyo-Joong; Hoshika, Shuichi; Kim, Myong-Jung; Carrigan, Matthew A; Benner, Steven A


    Expanding the synthetic biology of artificially expanded genetic information systems (AEGIS) requires tools to make and analyze RNA molecules having added nucleotide "letters". We report here the development of T7 RNA polymerase and reverse transcriptase to catalyze transcription and reverse transcription of xNA (DNA or RNA) having two complementary AEGIS nucleobases, 6-amino-5-nitropyridin-2-one (trivially, Z) and 2-aminoimidazo[1,2a]-1,3,5-triazin-4(8H)-one (trivially, P). We also report MALDI mass spectrometry and HPLC-based analyses for oligomeric GACUZP six-letter RNA and the use of ribonuclease (RNase) A and T1 RNase as enzymatic tools for the sequence-specific degradation of GACUZP RNA. We then applied these tools to analyze the GACUZP and GACTZP products of polymerases and reverse transcriptases (respectively) made from DNA and RNA templates. In addition to advancing this 6-letter AEGIS toward the biosynthesis of proteins containing additional amino acids, these experiments provided new insights into the biophysics of DNA.

  11. Heidegger and artificial intelligence

    Energy Technology Data Exchange (ETDEWEB)

    Diaz, G.


    The discipline of Artificial Intelligence, in its quest for machine intelligence, showed great promise as long as its areas of application were limited to problems of a scientific and situation neutral nature. The attempts to move beyond these problems to a full simulation of man's intelligence has faltered and slowed it progress, largely because of the inability of Artificial Intelligence to deal with human characteristic, such as feelings, goals, and desires. This dissertation takes the position that an impasse has resulted because Artificial Intelligence has never been properly defined as a science: its objects and methods have never been identified. The following study undertakes to provide such a definition, i.e., the required ground for Artificial Intelligence. The procedure and methods employed in this study are based on Heidegger's philosophy and techniques of analysis as developed in Being and Time. Results of this study show that both the discipline of Artificial Intelligence and the concerns of Heidegger in Being and Time have the same object; fundamental ontology. The application of Heidegger's conclusions concerning fundamental ontology unites the various aspects of Artificial Intelligence and provides the articulation which shows the parts of this discipline and how they are related.

  12. De novo design, synthesis and spectroscopic characterization of chiral benzimidazole-derived amino acid Zn(II) complexes: Development of tryptophan-derived specific hydrolytic DNA artificial nuclease agent (United States)

    Parveen, Shazia; Arjmand, Farukh


    Novel ternary dizinc(II) complexes 1- 3, derived from 1,2-bis(1H-benzimidazol-2-yl)ethane-1,2-diol and L-form of amino acids (viz., tryptophan, leucine and valine) were synthesized and characterized by spectroscopic (IR, 1H NMR, UV-vis, ESI-MS) and other analytical methods. To evaluate the biological preference of chiral drugs for inherently chiral target DNA, interaction of 1- 3 with calf thymus DNA in Tris-HCl buffer was studied by various biophysical techniques which reveal that all these complexes bind to CT DNA non-covalently via electrostatic interaction. The higher Kb value of L-tryptophan complex 1 suggested greater DNA binding propensity. Further, to evaluate the mode of action at the molecular level, interaction studies of complexes 1 and 2 with nucleotides (5'-GMP and 5'-TMP) were carried out by UV-vis titrations, 1H and 31P NMR which implicates the preferential selectivity of these complexes to N3 of thymine rather than N7 of guanine. Furthermore, complex 1 exhibits efficient DNA cleavage with supercoiled pBR322. The complex 1 cleaves DNA efficiently involving hydrolytic cleavage pathway. Such chiral synthetic hydrolytic nucleases with asymmetric centers are gaining considerable attention owing to their importance in biotechnology and drug design, in particular to cleave DNA with sequence selectivity different from that of the natural enzymes.

  13. Leaf storage conditions and genomic DNA isolation efficiency in ...

    African Journals Online (AJOL)



    Mar 4, 2008 ... Storage of plant tissues for DNA is important to avoid degradation of DNA. Preliminary ..... cessful was when SDS based isolation protocol (Edwards ..... preservative facilitating DNA extraction from 'difficult' plants collected.

  14. DNA damage and autophagy

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States); Panayiotidis, Mihalis I. [School of Community Health Sciences, University of Nevada, Reno, NV 89557 (United States); Franco, Rodrigo, E-mail: [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States)


    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  15. Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA.

    Directory of Open Access Journals (Sweden)

    Bastiaan Star

    Full Text Available Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua, which forms interrupted palindromes consisting of reverse complementary sequence at the 5' and 3'-ends of sequencing reads. The palindromic sequences themselves have specific properties - the bases at the 5'-end align well to the reference genome, whereas extensive misalignments exists among the bases at the terminal 3'-end. The terminal 3' bases are artificial extensions likely caused by the occurrence of hairpin loops in single stranded DNA (ssDNA, which can be ligated and amplified in particular library creation protocols. We propose that such hairpin loops allow the inclusion of erroneous nucleotides, specifically at the 3'-end of DNA strands, with the 5'-end of the same strand providing the template. We also find these palindromes in previously published ancient DNA (aDNA datasets, albeit at varying and substantially lower frequencies. This artifact can negatively affect the yield of endogenous DNA in these types of samples and introduces sequence bias.

  16. DNA damage in plant herbarium tissue.

    NARCIS (Netherlands)

    Staats, M.; Cuenca, A.; Richardson, J.E.; Ginkel, R.V.; Petersen, G.; Seberg, O.; Bakker, F.T.


    Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplif

  17. Artificial intelligence in nanotechnology (United States)

    Sacha, G. M.; Varona, P.


    During the last decade there has been increasing use of artificial intelligence tools in nanotechnology research. In this paper we review some of these efforts in the context of interpreting scanning probe microscopy, the study of biological nanosystems, the classification of material properties at the nanoscale, theoretical approaches and simulations in nanoscience, and generally in the design of nanodevices. Current trends and future perspectives in the development of nanocomputing hardware that can boost artificial-intelligence-based applications are also discussed. Convergence between artificial intelligence and nanotechnology can shape the path for many technological developments in the field of information sciences that will rely on new computer architectures and data representations, hybrid technologies that use biological entities and nanotechnological devices, bioengineering, neuroscience and a large variety of related disciplines.

  18. Artificial muscles on heat (United States)

    McKay, Thomas G.; Shin, Dong Ki; Percy, Steven; Knight, Chris; McGarry, Scott; Anderson, Iain A.


    Many devices and processes produce low grade waste heat. Some of these include combustion engines, electrical circuits, biological processes and industrial processes. To harvest this heat energy thermoelectric devices, using the Seebeck effect, are commonly used. However, these devices have limitations in efficiency, and usable voltage. This paper investigates the viability of a Stirling engine coupled to an artificial muscle energy harvester to efficiently convert heat energy into electrical energy. The results present the testing of the prototype generator which produced 200 μW when operating at 75°C. Pathways for improved performance are discussed which include optimising the electronic control of the artificial muscle, adjusting the mechanical properties of the artificial muscle to work optimally with the remainder of the system, good sealing, and tuning the resonance of the displacer to minimise the power required to drive it.

  19. Artificial organ engineering

    CERN Document Server

    Annesini, Maria Cristina; Piemonte, Vincenzo; Turchetti, Luca


    Artificial organs may be considered as small-scale process plants, in which heat, mass and momentum transfer operations and, possibly, chemical transformations are carried out. This book proposes a novel analysis of artificial organs based on the typical bottom-up approach used in process engineering. Starting from a description of the fundamental physico-chemical phenomena involved in the process, the whole system is rebuilt as an interconnected ensemble of elemental unit operations. Each artificial organ is presented with a short introduction provided by expert clinicians. Devices commonly used in clinical practice are reviewed and their performance is assessed and compared by using a mathematical model based approach. Whilst mathematical modelling is a fundamental tool for quantitative descriptions of clinical devices, models are kept simple to remain focused on the essential features of each process. Postgraduate students and researchers in the field of chemical and biomedical engineering will find that t...

  20. Artificial vision workbench. (United States)

    Frenger, P


    Machine vision is an important component of medical systems engineering. Inexpensive miniature solid state cameras are now available. This paper describes how these devices can be used as artificial retinas, to take snapshots and moving pictures in monochrome or color. Used in pairs, they produce a stereoscopic field of vision and enable depth perception. Macular and peripheral vision can be simulated electronically. This paper also presents the author's design of an artificial orbit for this synthetic eye. The orbit supports the eye, protects it, and provides attachment points for the ocular motion control system. Convergence and image fusion can be produced, and saccades simulated, along with the other ocular motions. The use of lenses, filters, irises and focusing mechanisms are also discussed. Typical camera-computer interfaces are described, including the use of "frame grabbers" and analog-to-digital image conversion. Software programs for eye positioning, image manipulation, feature extraction and object recognition are discussed, including the application of artificial neural networks.

  1. Artificial intelligence in nanotechnology. (United States)

    Sacha, G M; Varona, P


    During the last decade there has been increasing use of artificial intelligence tools in nanotechnology research. In this paper we review some of these efforts in the context of interpreting scanning probe microscopy, the study of biological nanosystems, the classification of material properties at the nanoscale, theoretical approaches and simulations in nanoscience, and generally in the design of nanodevices. Current trends and future perspectives in the development of nanocomputing hardware that can boost artificial-intelligence-based applications are also discussed. Convergence between artificial intelligence and nanotechnology can shape the path for many technological developments in the field of information sciences that will rely on new computer architectures and data representations, hybrid technologies that use biological entities and nanotechnological devices, bioengineering, neuroscience and a large variety of related disciplines.

  2. General artificial neuron (United States)

    Degeratu, Vasile; Schiopu, Paul; Degeratu, Stefania


    In this paper the authors present a model of artificial neuron named the general artificial neuron. Depending on application this neuron can change self number of inputs, the type of inputs (from excitatory in inhibitory or vice versa), the synaptic weights, the threshold, the type of intensifying functions. It is achieved into optoelectronic technology. Also, into optoelectronic technology a model of general McCulloch-Pitts neuron is showed. The advantages of these neurons are very high because we have to solve different applications with the same neural network, achieved from these neurons, named general neural network.

  3. Spatially Resolved Artificial Chemistry

    DEFF Research Database (Denmark)

    Fellermann, Harold


    Although spatial structures can play a crucial role in chemical systems and can drastically alter the outcome of reactions, the traditional framework of artificial chemistry is a well-stirred tank reactor with no spatial representation in mind. Advanced method development in physical chemistry has...... made a class of models accessible to the realms of artificial chemistry that represent reacting molecules in a coarse-grained fashion in continuous space. This chapter introduces the mathematical models of Brownian dynamics (BD) and dissipative particle dynamics (DPD) for molecular motion and reaction...

  4. Artificial Photosynthesis: Hybrid Systems. (United States)

    Ni, Yan; Hollmann, Frank

    Oxidoreductases are promising catalysts for organic synthesis. To sustain their catalytic cycles they require efficient supply with redox equivalents. Today classical biomimetic approaches utilizing natural electron supply chains prevail but artificial regeneration approaches bear the promise of simpler and more robust reaction schemes. Utilizing visible light can accelerate such artificial electron transport chains and even enable thermodynamically unfeasible reactions such as the use of water as reductant.This contribution critically summarizes the current state of the art in photoredoxbiocatalysis (i.e. light-driven biocatalytic oxidation and reduction reactions).

  5. Artificial human vision. (United States)

    Dowling, Jason


    Can vision be restored to the blind? As early as 1929 it was discovered that stimulating the visual cortex of an individual led to the perception of spots of light, known as phosphenes [1] . The aim of artificial human vision systems is to attempt to utilize the perception of phosphenes to provide a useful substitute for normal vision. Currently, four locations for electrical stimulation are being investigated; behind the retina (subretinal), in front of the retina (epiretinal), the optic nerve and the visual cortex (using intra- and surface electrodes). This review discusses artificial human vision technology and requirements, and reviews the current development projects.

  6. Bayesian artificial intelligence

    CERN Document Server

    Korb, Kevin B


    As the power of Bayesian techniques has become more fully realized, the field of artificial intelligence has embraced Bayesian methodology and integrated it to the point where an introduction to Bayesian techniques is now a core course in many computer science programs. Unlike other books on the subject, Bayesian Artificial Intelligence keeps mathematical detail to a minimum and covers a broad range of topics. The authors integrate all of Bayesian net technology and learning Bayesian net technology and apply them both to knowledge engineering. They emphasize understanding and intuition but also provide the algorithms and technical background needed for applications. Software, exercises, and solutions are available on the authors' website.

  7. Artificial intelligence in cardiology. (United States)

    Bonderman, Diana


    Decision-making is complex in modern medicine and should ideally be based on available data, structured knowledge and proper interpretation in the context of an individual patient. Automated algorithms, also termed artificial intelligence that are able to extract meaningful patterns from data collections and build decisions upon identified patterns may be useful assistants in clinical decision-making processes. In this article, artificial intelligence-based studies in clinical cardiology are reviewed. The text also touches on the ethical issues and speculates on the future roles of automated algorithms versus clinicians in cardiology and medicine in general.

  8. Extracting biological knowledge from DNA sequences

    Energy Technology Data Exchange (ETDEWEB)

    De La Vega, F.M. [CINVESTAV-IPN (Mexico); Thieffry, D. [Universite Libre de Bruxelles, Rhode-Saint-Genese (Belgium)]|[Universidad Nacional Autonoma de Mexico, Morelos (Mexico); Collado-Vides, J. [Universidad Nacional Autonoma de Mexico, Morelos (Mexico)


    This session describes the elucidation of information from dna sequences and what challenges computational biologists face in their task of summarizing and deciphering the human genome. Techniques discussed include methods from statistics, information theory, artificial intelligence and linguistics. 1 ref.

  9. Cultivation-independent identification of candidate dehalorespiring bacteria in tetrachloroethylene degradation. (United States)

    Yamasaki, Shouhei; Nomura, Nobuhiko; Nakajima, Toshiaki; Uchiyama, Hiroo


    Tetrachloroethylene (PCE) is one of the major pollutants and is degraded by dissimilation by dehalorespiring bacteria. The dehalorespiring bacteria are anaerobic, and most cannot be cultured by conventional agar plating methods. Therefore, to identify the dehalorespiring bacteria that dissimilatively degrade PCE, a cultivation-independent method is required. To achieve accurate and detailed analysis of the bacteria, we developed a novel stable isotope probing (SIP) method. This technique involves 2 steps, namely, a labeling step, in which a labeled carbon source is incorporated into the sample's DNA, and an analysis step, in which the DNA is isolated, fractionated, and analyzed by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). Subsequently, 16S rRNA sequencing and phylogenetic analysis were performed to identify the bacteria. Initially, we examined the effectiveness of this method by using Dehalococcoides ethenogenes 195 consortium as a defined model system. The result indicated the method was able to correctly identify the dehalorespiring bacteria D. ethenogenes 195 from the consortium. Moreover, in an artificially contaminated microcosm experiment, we confirmed that the method was able to identify the indigenous dehalorespiring bacteria Dehalobacter sp. Thus, we concluded that this novel method was a feasible tool to identify dehalorespiring bacteria in natural environments.

  10. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan


    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  11. Degradation of endocrine disrupting chemicals by genetic transformants with two lignin degrading enzymes in Phlebia tremellosa. (United States)

    Kum, Hyunwoo; Lee, Sungsuk; Ryu, Sunhwa; Choi, Hyoung T


    A white rot fungus Phlebia tremellosa produced lignin degrading enzymes, which showed degrading activity against various recalcitrant compounds. However, manganese peroxidase (MnP) activity, one of lignin degrading enzymes, was very low in this fungus under various culture conditions. An expression vector that carried both the laccase and MnP genes was constructed using laccase genomic DNA of P. tremellosa and MnP cDNA from Polyporus brumalis. P. tremellosa was genetically transformed using the expression vector to obtain fungal transformants showing increased laccase and MnP activity. Many transformants showed highly increased laccase and MnP activity at the same time in liquid medium, and three of them were used to degrade endocrine disrupting chemicals. The transformant not only degraded bisphenol A and nonylphenol more rapidly but also removed the estrogenic activities of the chemicals faster than the wild type strain.

  12. Artificial Left Ventricle

    CERN Document Server

    Ranjbar, Saeed; Meybodi, Mahmood Emami


    This Artificial left ventricle is based on a simple conic assumption shape for left ventricle where its motion is made by attached compressed elastic tubes to its walls which are regarded to electrical points at each nodal .This compressed tubes are playing the role of myofibers in the myocardium of the left ventricle. These elastic tubes have helical shapes and are transacting on these helical bands dynamically. At this invention we give an algorithm of this artificial left ventricle construction that of course the effect of the blood flow in LV is observed with making beneficiary used of sensors to obtain this effecting, something like to lifegates problem. The main problem is to evaluate powers that are interacted between elastic body (left ventricle) and fluid (blood). The main goal of this invention is to show that artificial heart is not just a pump, but mechanical modeling of LV wall and its interaction with blood in it (blood movement modeling) can introduce an artificial heart closed to natural heart...

  13. Artificial Gravity Research Plan (United States)

    Gilbert, Charlene


    This document describes the forward working plan to identify what countermeasure resources are needed for a vehicle with an artificial gravity module (intermittent centrifugation) and what Countermeasure Resources are needed for a rotating transit vehicle (continuous centrifugation) to minimize the effects of microgravity to Mars Exploration crewmembers.

  14. Artificial intelligence and psychiatry. (United States)

    Servan-Schreiber, D


    This paper provides a brief historical introduction to the new field of artificial intelligence and describes some applications to psychiatry. It focuses on two successful programs: a model of paranoid processes and an expert system for the pharmacological management of depressive disorders. Finally, it reviews evidence in favor of computerized psychotherapy and offers speculations on the future development of research in this area.

  15. Observations of artificial satellites

    Directory of Open Access Journals (Sweden)



    Full Text Available The following publication gives the results of photographic
    observations of artificial satellites made at Asiago during the second
    and third year of this programme. The fixed camera technique and that
    with moving film (the latter still in its experimental stage have been used.

  16. Micromachined Artificial Haircell (United States)

    Liu, Chang (Inventor); Engel, Jonathan (Inventor); Chen, Nannan (Inventor); Chen, Jack (Inventor)


    A micromachined artificial sensor comprises a support coupled to and movable with respect to a substrate. A polymer, high-aspect ratio cilia-like structure is disposed on and extends out-of-plane from the support. A strain detector is disposed with respect to the support to detect movement of the support.

  17. Artificial recharge of groundwater (United States)

    The Task Committee on Guidelines for Artificial Recharge of Groundwater, of the American Society of Civil Engineers' (ASCE) Irrigation and Drainage Division, sponsored an International Symposium on Artificial Recharge of Groundwater at the Inn-at-the-Park Hotel in Anaheim, Calif., August 23-27, 1988. Cosponsors were the U.S. Geological Survey, California Department of Water Resources, University of California Water Resources Center, Metropolitan Water District of Southern California, with cooperation from the U.S. Bureau of Reclamation, International Association of Hydrological Sciences, American Water Resources Association, U.S. Agency for International Development, World Bank, United Nations Department of Technical Cooperation for Development, and a number of local and state organizations.Because of the worldwide interest in artificial recharge and the need to develop efficient recharge facilities, the Anaheim symposium brought together an interdisciplinary group of engineers and scientists to provide a forum for many professional disciplines to exchange experiences and findings related to various types of artificial recharge; learn from both successful and unsuccessful case histories; promote technology transfer between the various disciplines; provide an education resource for communication with those who are not water scientists, such as planners, lawyers, regulators, and the public in general; and indicate directions by which cities or other entities can save funds by having reasonable technical guidelines for implementation of a recharge project.

  18. Artificial intelligence within AFSC (United States)

    Gersh, Mark A.


    Information on artificial intelligence research in the Air Force Systems Command is given in viewgraph form. Specific research that is being conducted at the Rome Air Development Center, the Space Technology Center, the Human Resources Laboratory, the Armstrong Aerospace Medical Research Laboratory, the Armamant Laboratory, and the Wright Research and Development Center is noted.

  19. Introduction to Artificial Neural Networks

    DEFF Research Database (Denmark)

    Larsen, Jan


    The note addresses introduction to signal analysis and classification based on artificial feed-forward neural networks.......The note addresses introduction to signal analysis and classification based on artificial feed-forward neural networks....

  20. Kink solitons in DNA

    CERN Document Server

    Zdravković, S; Daniel, M


    We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose possible experimental assays based on single molecule micromanipulation techniques. The aim of these experiments is to excite the rotational waves and to determine their speeds along excited DNA. We propose that these experiments should be conducted either for the case of double stranded (DS) or single stranded (SS) DNA. A key question is to compare the corresponding velocities of the rotational waves indicating which one is bigger. The ratio of these velocities appears to be related with the sign of the model parameter representing ratio of the hydrogen-bonding and the covalent-bonding interaction within the considered DNA chain.

  1. Wide Band Artificial Pulsar (United States)

    Parsons, Zackary


    The Wide Band Artificial Pulsar (WBAP) is an instrument verification device designed and built by the National Radio Astronomy Observatory (NRAO) in Green Bank, West Virgina. The site currently operates the Green Bank Ultimate Pulsar Processing Instrument (GUPPI) and the Versatile Green Bank Astronomical Spectrometer (VEGAS) digital backends for their radio telescopes. The commissioning and continued support for these sophisticated backends has demonstrated a need for a device capable of producing an accurate artificial pulsar signal. The WBAP is designed to provide a very close approximation to an actual pulsar signal. This presentation is intended to provide an overview of the current hardware and software implementations and to also share the current results from testing using the WBAP.

  2. Artificial Neural Network

    Directory of Open Access Journals (Sweden)

    Kapil Nahar


    Full Text Available An artificial neural network is an information-processing paradigm that is inspired by the way biological nervous systems, such as the brain, process information.The key element of this paradigm is the novel structure of the information processing system. It is composed of a large number of highly interconnected processing elements (neurons working in unison to solve specific problems.Ann’s, like people, learn by example.

  3. Essentials of artificial intelligence

    CERN Document Server

    Ginsberg, Matt


    Since its publication, Essentials of Artificial Intelligence has beenadopted at numerous universities and colleges offering introductory AIcourses at the graduate and undergraduate levels. Based on the author'scourse at Stanford University, the book is an integrated, cohesiveintroduction to the field. The author has a fresh, entertaining writingstyle that combines clear presentations with humor and AI anecdotes. At thesame time, as an active AI researcher, he presents the materialauthoritatively and with insight that reflects a contemporary, first hand

  4. Artificial Neural Network

    Directory of Open Access Journals (Sweden)

    Kapil Nahar


    Full Text Available An artificial neural network is an information-processing paradigm that is inspired by the way biological nervous systems, such as the brain, process information. The key element of this paradigm is the novel structure of the information processing system. It is composed of a large number of highly interconnected processing elements (neurons working in unison to solve specific problems. Ann’s, like people, learn by example.

  5. Artificial neural network modelling

    CERN Document Server

    Samarasinghe, Sandhya


    This book covers theoretical aspects as well as recent innovative applications of Artificial Neural networks (ANNs) in natural, environmental, biological, social, industrial and automated systems. It presents recent results of ANNs in modelling small, large and complex systems under three categories, namely, 1) Networks, Structure Optimisation, Robustness and Stochasticity 2) Advances in Modelling Biological and Environmental Systems and 3) Advances in Modelling Social and Economic Systems. The book aims at serving undergraduates, postgraduates and researchers in ANN computational modelling. .

  6. Artificial sweetener; Jinko kanmiryo

    Energy Technology Data Exchange (ETDEWEB)



    The patents related to the artificial sweetener that it is introduced to the public in 3 years from 1996 until 1998 are 115 cases. The sugar quality which makes an oligosaccharide and sugar alcohol the subject is greatly over 28 cases of the non-sugar quality in the one by the kind as a general tendency of these patents at 73 cases in such cases as the Aspartame. The method of manufacture patent, which included new material around other peptides, the oligosaccharide and sugar alcohol isn`t inferior to 56 cases of the formation thing patent at 43 cases, and pays attention to the thing, which is many by the method of manufacture, formation. There is most improvement of the quality of sweetness with 31 cases in badness of the aftertaste which is characteristic of the artificial sweetener and so on, and much stability including the improvement in the flavor of food by the artificial sweetener, a long time and dissolution, fluid nature and productivity and improvement of the economy such as a cost are seen with effect on a purpose. (NEDO)


    Directory of Open Access Journals (Sweden)

    A. L. M Marinho


    Full Text Available This literature review aims to show the main scientific advances achieved in the area of Artificial Insemination (AI within animal reproduction and how these can improve reproductive efficiency and productive of the Brazilian cattle herd. With knowledge of the mechanisms involved in the control of reproductive physiology, in levels endocrine, cellular and molecular, it was possible the development of reproductive biotechnologies, standing out the IA, It has been used on a large scale, by allow the multiplication of animals superior genetically , increase the birthrate and be particularly effective in adjusting the breeding season in cattle. Artificial insemination has an important role in animal genetic improvement; it is the main and more viable middle of spread of genes worldwide when compared to other methods how technologies of embryos and the natural breeding. There are several advantages in using artificial insemination in herd both of cutting as milkman, as herd genetic improvement in lesser time and at a low cost through the use of semen of demonstrably superior sires for production, well as in the control and decrease of diseases which entail reproductive losses and consequently productive, by allowing the creator The crossing of zebuine females with bulls of European breeds and vice-versa, through the use of semen, increasing the number of progeny of a reproducer superior

  8. Microbial Degradation of Organic Wastes at Low Temperatures.

    Directory of Open Access Journals (Sweden)

    K.V. Ramana


    Full Text Available Microbial degradation of organic wastes mainly comprising animal and human wastes, is drastically reduced at extreme low temperatures. For the biodegradation of these wastes, technological inputs are required from disciplines like microbiology, biochemistry, molecular biology, digester modelling and heat transfer at extreme low temperature climates. Various steps in the process of biodegradation have to be studied to formulate an effective organic waste disposal method. Anaerobic digestion of organic wastes is preferred over aerobic waste treatment method, since it yields biogas as a by-product, which in turn can be utilised for heating the digester contents to increase its efficiency. Furthermore, one of the possibilities that can be explored is the utilisation of high rate anaerobic digesters which maintain temperature by means of artificial heating. It is either met by non-conventional energy sources, such as solar and wind energy, or by expending liquid fuels. In addition, insulation of the digester with polymeric materials and immobilisation of slow growing bacterial population may enhance the digester performance to a great extent. In spite of several developments, inoculum adaptation is considered to be one of the essential steps for low temperature anaerobic digestion to obtain methane as a by-product. With advancements in recombinant DNA technology, it may be possible to increase the efficiency of various microbial population that take part in the anaerobic digestion. However, till date, the options available for low temperature biodegradation are digester insulation, inoculum adaptation, and use of high rate/second-generation digesters.

  9. Lactobacillus sps. lipase mediated poly (ε-caprolactone) degradation. (United States)

    Khan, Imran; Ray Dutta, Jayati; Ganesan, Ramakrishnan


    Polymer degradation through lipase appears to be an enthralling alternative to bulk chemical routes. Poly (ε-caprolactone) (PCL) is an artificial polyester that can be degraded by microbes and enzymes like lipases and esterases. The environmental degradation of PCL is dependent on the activity of bacteria that characterization techniques such as thermogravimetric analysis, differential thermal are widely present in the ecosystem. In this study, three different lipases derived from Lactobacillus brevis, Lactobacillus plantarum and their co-culture have been utilized to explore their efficiency towards PCL enzymatic degradation. The effect of parameters such as enzyme loading and degradation time has been explored to understand the efficiency of the enzymes used in this study. Various analysis, scanning electron microscopy and Fourier transform infrared spectroscopy have been employed to study the enzymatic degradation and its possible mechanistic insight.

  10. [Fibrin(ogen degradation product concentration (SFP) as a diagnostic parameter for the differentiation of artifical and essential blood in cerebrospinal fluid]. (United States)

    Hindersin, P; Heidrich, R


    The fibrin(ogen) degradation product concentration is another differential-diagnosis parameter for distinguishing between artificially blood-stained and essentially blood-stained CSF. Determination of the fibrin(ogen) degradation product concentration has been found to be a reliable method of recognizing natively and artificially blood-stained CSF as being different.

  11. Bacterial Artificial Chromosome Mutagenesis Using Recombineering

    Directory of Open Access Journals (Sweden)

    Kumaran Narayanan


    Full Text Available Gene expression from bacterial artificial chromosome (BAC clones has been demonstrated to facilitate physiologically relevant levels compared to viral and nonviral cDNA vectors. BACs are large enough to transfer intact genes in their native chromosomal setting together with flanking regulatory elements to provide all the signals for correct spatiotemporal gene expression. Until recently, the use of BACs for functional studies has been limited because their large size has inherently presented a major obstacle for introducing modifications using conventional genetic engineering strategies. The development of in vivo homologous recombination strategies based on recombineering in E. coli has helped resolve this problem by enabling facile engineering of high molecular weight BAC DNA without dependence on suitably placed restriction enzymes or cloning steps. These techniques have considerably expanded the possibilities for studying functional genetics using BACs in vitro and in vivo.

  12. Developmental validation of the HIrisPlex system: DNA-based eye and hair colour prediction for forensic and anthropological usage. (United States)

    Walsh, Susan; Chaitanya, Lakshmi; Clarisse, Lindy; Wirken, Laura; Draus-Barini, Jolanta; Kovatsi, Leda; Maeda, Hitoshi; Ishikawa, Takaki; Sijen, Titia; de Knijff, Peter; Branicki, Wojciech; Liu, Fan; Kayser, Manfred


    Forensic DNA Phenotyping or 'DNA intelligence' tools are expected to aid police investigations and find unknown individuals by providing information on externally visible characteristics of unknown suspects, perpetrators and missing persons from biological samples. This is especially useful in cases where conventional DNA profiling or other means remain non-informative. Recently, we introduced the HIrisPlex system, capable of predicting both eye and hair colour from DNA. In the present developmental validation study, we demonstrate that the HIrisPlex assay performs in full agreement with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines providing an essential prerequisite for future HIrisPlex applications to forensic casework. The HIrisPlex assay produces complete profiles down to only 63 pg of DNA. Species testing revealed human specificity for a complete HIrisPlex profile, while only non-human primates showed the closest full profile at 20 out of the 24 DNA markers, in all animals tested. Rigorous testing of simulated forensic casework samples such as blood, semen, saliva stains, hairs with roots as well as extremely low quantity touch (trace) DNA samples, produced complete profiles in 88% of cases. Concordance testing performed between five independent forensic laboratories displayed consistent reproducible results on varying types of DNA samples. Due to its design, the assay caters for degraded samples, underlined here by results from artificially degraded DNA and from simulated casework samples of degraded DNA. This aspect was also demonstrated previously on DNA samples from human remains up to several hundreds of years old. With this paper, we also introduce enhanced eye and hair colour prediction models based on enlarged underlying databases of HIrisPlex genotypes and eye/hair colour phenotypes (eye colour: N = 9188 and hair colour: N = 1601). Furthermore, we present an online web-based system for individual eye and hair colour

  13. Quantification of human mitochondrial DNA using synthesized DNA standards. (United States)

    Kavlick, Mark F; Lawrence, Helen S; Merritt, R Travis; Fisher, Constance; Isenberg, Alice; Robertson, James M; Budowle, Bruce


    Successful mitochondrial DNA (mtDNA) forensic analysis depends on sufficient quantity and quality of mtDNA. A real-time quantitative PCR assay was developed to assess such characteristics in a DNA sample, which utilizes a duplex, synthetic DNA to ensure optimal quality assurance and quality control. The assay's 105-base pair target sequence facilitates amplification of degraded DNA and is minimally homologous to nonhuman mtDNA. The primers and probe hybridize to a region that has relatively few sequence polymorphisms. The assay can also identify the presence of PCR inhibitors and thus indicate the need for sample repurification. The results show that the assay provides information down to 10 copies and provides a dynamic range spanning seven orders of magnitude. Additional experiments demonstrated that as few as 300 mtDNA copies resulted in successful hypervariable region amplification, information that permits sample conservation and optimized downstream PCR testing. The assay described is rapid, reliable, and robust.

  14. Repair and degradation systems in irradiated animal cells

    Energy Technology Data Exchange (ETDEWEB)

    Ivannik, B.P.; Proskuryakov, S.Ya.; Ryabchenko, N.I. (Akademiya Meditsinskikh Nauk SSSR, Obninsk. Nauchno-Issledovatel' skij Inst. Meditsinskoj Radiologii)

    It was shown that primary radiosensitivity of DNA depends on the rate of DNA repair. In Zajdela hepatoma cells, cycloheximide administered immediately or 2 h before irradiation of animals does not influence DNA repair. Cycloheximide administered 4 h before irradiation of rats with a dose of 30 Gy arrests DNA repair in thymocytes and Zajdela hepatoma cells. At the same time, in cells of rat lymph nodes and spleen, under similar conditions, cycloheximide does not influence DNA repair and inhibits the secondary DNA degradation.

  15. Damage and repair of ancient DNA

    DEFF Research Database (Denmark)

    Mitchell, David; Willerslev, Eske; Hansen, Anders


    , and extensive degradation. In the course of this review, we will discuss the current aDNA literature describing the importance of aDNA studies as they relate to important biological questions and the difficulties associated with extracting useful information from highly degraded and damaged substrates derived......Under certain conditions small amounts of DNA can survive for long periods of time and can be used as polymerase chain reaction (PCR) substrates for the study of phylogenetic relationships and population genetics of extinct plants and animals, including hominids. Because of extensive DNA...... degradation, these studies are limited to species that lived within the past 10(4)-10(5) years (Late Pleistocene), although DNA sequences from 10(6) years have been reported. Ancient DNA (aDNA) has been used to study phylogenetic relationships of protists, fungi, algae, plants, and higher eukaryotes...

  16. Studies on the sonic degradation of deoxyribonucleic acid. (United States)



    T7 DNA was partially degraded by x-rays, DNAase, and sonic irradiation. The molecular weight distributions were calculated from sedimentation velocity studies on the resulting preparations. Comparison with the theoretical curve derived by Montroll and Simha showed that the first two degradative methods act grossly at random, whereas sonication is a non-random process resulting in the preferential halving of the DNA molecules in solution.

  17. Degradation kinetics of ptaquiloside in soil and soil solution

    DEFF Research Database (Denmark)

    Ovesen, Rikke Gleerup; Rasmussen, Lars Holm; Hansen, Hans Christian Bruun


    by clay silicates. Ptaquiloside appeared to be stable in all soil solutions, in which no degradation was observed within a period of 28 d, in strong contrast to previous studies of hydrolysis rates in artificial aqueous electrolytes. The present study predicts that the risk of PTA leaching is controlled...

  18. Bayesian artificial intelligence

    CERN Document Server

    Korb, Kevin B


    Updated and expanded, Bayesian Artificial Intelligence, Second Edition provides a practical and accessible introduction to the main concepts, foundation, and applications of Bayesian networks. It focuses on both the causal discovery of networks and Bayesian inference procedures. Adopting a causal interpretation of Bayesian networks, the authors discuss the use of Bayesian networks for causal modeling. They also draw on their own applied research to illustrate various applications of the technology.New to the Second EditionNew chapter on Bayesian network classifiersNew section on object-oriente

  19. Uncertainty in artificial intelligence

    CERN Document Server

    Kanal, LN


    How to deal with uncertainty is a subject of much controversy in Artificial Intelligence. This volume brings together a wide range of perspectives on uncertainty, many of the contributors being the principal proponents in the controversy.Some of the notable issues which emerge from these papers revolve around an interval-based calculus of uncertainty, the Dempster-Shafer Theory, and probability as the best numeric model for uncertainty. There remain strong dissenting opinions not only about probability but even about the utility of any numeric method in this context.

  20. Polymer artificial muscles

    Directory of Open Access Journals (Sweden)

    Tissaphern Mirfakhrai


    Full Text Available The various types of natural muscle are incredible material systems that enable the production of large deformations by repetitive molecular motions. Polymer artificial muscle technologies are being developed that produce similar strains and higher stresses using electrostatic forces, electrostriction, ion insertion, and molecular conformational changes. Materials used include elastomers, conducting polymers, ionically conducting polymers, and carbon nanotubes. The mechanisms, performance, and remaining challenges associated with these technologies are described. Initial applications are being developed, but further work by the materials community should help make these technologies applicable in a wide range of devices where muscle-like motion is desirable.

  1. Artificial intelligence: Human effects

    Energy Technology Data Exchange (ETDEWEB)

    Yazdani, M.; Narayanan, A.


    This book presents an up-to-date study of the interaction between the fast-growing discipline of artificial intelligence and other human endeavors. The volume explores the scope and limitations of computing, and presents a history of the debate on the possibility of machines achieving intelligence. The authors offer a state-of-the-art survey of Al, concentrating on the ''mind'' (language understanding) and the ''body'' (robotics) of intelligent computing systems.

  2. Mechanism of artificial heart

    CERN Document Server

    Yamane, Takashi


    This book first describes medical devices in relation to regenerative medicine before turning to a more specific topic: artificial heart technologies. Not only the pump mechanisms but also the bearing, motor mechanisms, and materials are described, including expert information. Design methods are described to enhance hemocompatibility: main concerns are reduction of blood cell damage and protein break, as well as prevention of blood clotting. Regulatory science from R&D to clinical trials is also discussed to verify the safety and efficacy of the devices.

  3. Characterization of Streptococcus salivarius growth and maintenance in artificial saliva. (United States)

    Roger, P; Delettre, J; Bouix, M; Béal, C


    To help gain a better understanding of factors influencing the establishment within the oral cavity of Streptococcus salivarius K12, a commensal oral bacterium, we characterized its behaviour in artificial saliva. Streptococcus salivarius K12 was grown in artificial saliva complemented with a representative meal, under oral pH and temperature conditions. Exponential growth phase was characterized by a high specific growth rate (2.8 h(-1)). During maintenance phase, an uncoupling between growth and lactic acid production occurred, which allowed maintaining viability (95%), intracellular pH (6.6) and membrane polarisation (95%), and thus proton motive force. However, in late stationary phase, viability (64%) and vitality were degraded as a result of lower synthesis of energetic and glycogen-related proteins as compared to a richer medium. Streptococcus salivarius was able to rapidly grow in complemented artificial saliva. Nevertheless, a degradation of its physiological state was observed in late-stationary phase. This work demonstrates, for the first time, that artificial saliva was a convenient medium that permitted Strep. salivarius to grow in oral conditions (physico-chemical environment, addition of meals) but not to maintain cellular viability and vitality in starvation conditions. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

  4. Optical monitoring the degradation of PLGA inverse opal film

    Institute of Scientific and Technical Information of China (English)

    Li-Guo Sun; Zhuo-Ying Xie; Yuan-Jin Zhao; Hong-Mei Wei; Zhong-Ze Gu


    Implantable materials have broad applications in tissue engineering and in vivo sensors.It is essential to know the detailed information of the implantable materials during their degradation.In this paper,we developed a method to monitor the degradation process of a well-used biomaterial,poly(lactide-coglycolide) (PLGA) by taking advantage of inverse opal structure.We found that mass loss,molecular weight and glass transition temperature of PLGA during the degradation process in Hank's artificial body fluid can be in situ monitored by measuring the optical properties of PLGA inverse opal.

  5. How to teach artificial organs. (United States)

    Zapanta, Conrad M; Borovetz, Harvey S; Lysaght, Michael J; Manning, Keefe B


    Artificial organs education is often an overlooked field for many bioengineering and biomedical engineering students. The purpose of this article is to describe three different approaches to teaching artificial organs. This article can serve as a reference for those who wish to offer a similar course at their own institutions or incorporate these ideas into existing courses. Artificial organ classes typically fulfill several ABET (Accreditation Board for Engineering and Technology) criteria, including those specific to bioengineering and biomedical engineering programs.

  6. Parallel artificial liquid membrane extraction

    DEFF Research Database (Denmark)

    Gjelstad, Astrid; Rasmussen, Knut Einar; Parmer, Marthe Petrine


    This paper reports development of a new approach towards analytical liquid-liquid-liquid membrane extraction termed parallel artificial liquid membrane extraction. A donor plate and acceptor plate create a sandwich, in which each sample (human plasma) and acceptor solution is separated by an arti...... by an artificial liquid membrane. Parallel artificial liquid membrane extraction is a modification of hollow-fiber liquid-phase microextraction, where the hollow fibers are replaced by flat membranes in a 96-well plate format....

  7. Trimaran Resistance Artificial Neural Network (United States)


    11th International Conference on Fast Sea Transportation FAST 2011, Honolulu, Hawaii, USA, September 2011 Trimaran Resistance Artificial Neural Network Richard...Trimaran Resistance Artificial Neural Network 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e... Artificial Neural Network and is restricted to the center and side-hull configurations tested. The value in the parametric model is that it is able to

  8. Artificial Intelligence in Space Platforms. (United States)


    computer algorithms, there still appears to be a need for Artificial Inteligence techniques in the navigation area. The reason is that navigaion, in...RD-RI32 679 ARTIFICIAL INTELLIGENCE IN SPACE PLRTFORNSMU AIR FORCE 1/𔃼 INST OF TECH WRIGHT-PRTTERSON AFB OH SCHOOL OF ENGINEERING M A WRIGHT DEC 94...i4 Preface The purpose of this study was to analyze the feasibility of implementing Artificial Intelligence techniques to increase autonomy for

  9. DNA recognition by synthetic constructs. (United States)

    Pazos, Elena; Mosquera, Jesús; Vázquez, M Eugenio; Mascareñas, José L


    The interaction of transcription factors with specific DNA sites is key for the regulation of gene expression. Despite the availability of a large body of structural data on protein-DNA complexes, we are still far from fully understanding the molecular and biophysical bases underlying such interactions. Therefore, the development of non-natural agents that can reproduce the DNA-recognition properties of natural transcription factors remains a major and challenging goal in chemical biology. In this review we summarize the basics of double-stranded DNA recognition by transcription factors, and describe recent developments in the design and preparation of synthetic DNA binders. We mainly focus on synthetic peptides that have been designed by following the DNA interaction of natural proteins, and we discuss how the tools of organic synthesis can be used to make artificial constructs equipped with functionalities that introduce additional properties to the recognition process, such as sensing and controllability.

  10. [Artificial neural networks in Neurosciences]. (United States)

    Porras Chavarino, Carmen; Salinas Martínez de Lecea, José María


    This article shows that artificial neural networks are used for confirming the relationships between physiological and cognitive changes. Specifically, we explore the influence of a decrease of neurotransmitters on the behaviour of old people in recognition tasks. This artificial neural network recognizes learned patterns. When we change the threshold of activation in some units, the artificial neural network simulates the experimental results of old people in recognition tasks. However, the main contributions of this paper are the design of an artificial neural network and its operation inspired by the nervous system and the way the inputs are coded and the process of orthogonalization of patterns.

  11. DNA Polymer Brush Patterning through Photocontrollable Surface-Initiated DNA Hybridization Chain Reaction. (United States)

    Huang, Fujian; Zhou, Xiang; Yao, Dongbao; Xiao, Shiyan; Liang, Haojun


    The fabrication of DNA polymer brushes with spatial resolution onto a solid surface is a crucial step for biochip research and related applications, cell-free gene expression study, and even artificial cell fabrication. Here, for the first time, a DNA polymer brush patterning method is reported based on the photoactivation of an ortho-nitrobenzyl linker-embedded DNA hairpin structure and a subsequent surface-initiated DNA hybridization chain reaction (HCR). Inert DNA hairpins are exposed to ultraviolet light irradiation to generate DNA duplexes with two active sticky ends (toeholds) in a programmable manner. These activated DNA duplexes can initiate DNA HCR to generate multifunctional patterned DNA polymer brushes with complex geometrical shapes. Different multifunctional DNA polymer brush patterns can be fabricated on certain areas of the same solid surface using this method. Moreover, the patterned DNA brush surface can be used to capture target molecules in a desired manner.

  12. The total artificial heart. (United States)

    Cook, Jason A; Shah, Keyur B; Quader, Mohammed A; Cooke, Richard H; Kasirajan, Vigneshwar; Rao, Kris K; Smallfield, Melissa C; Tchoukina, Inna; Tang, Daniel G


    The total artificial heart (TAH) is a form of mechanical circulatory support in which the patient's native ventricles and valves are explanted and replaced by a pneumatically powered artificial heart. Currently, the TAH is approved for use in end-stage biventricular heart failure as a bridge to heart transplantation. However, with an increasing global burden of cardiovascular disease and congestive heart failure, the number of patients with end-stage heart failure awaiting heart transplantation now far exceeds the number of available hearts. As a result, the use of mechanical circulatory support, including the TAH and left ventricular assist device (LVAD), is growing exponentially. The LVAD is already widely used as destination therapy, and destination therapy for the TAH is under investigation. While most patients requiring mechanical circulatory support are effectively treated with LVADs, there is a subset of patients with concurrent right ventricular failure or major structural barriers to LVAD placement in whom TAH may be more appropriate. The history, indications, surgical implantation, post device management, outcomes, complications, and future direction of the TAH are discussed in this review.

  13. Development of artificial empathy. (United States)

    Asada, Minoru


    We have been advocating cognitive developmental robotics to obtain new insight into the development of human cognitive functions by utilizing synthetic and constructive approaches. Among the different emotional functions, empathy is difficult to model, but essential for robots to be social agents in our society. In my previous review on artificial empathy (Asada, 2014b), I proposed a conceptual model for empathy development beginning with emotional contagion to envy/schadenfreude along with self/other differentiation. In this article, the focus is on two aspects of this developmental process, emotional contagion in relation to motor mimicry, and cognitive/affective aspects of the empathy. It begins with a summary of the previous review (Asada, 2014b) and an introduction to affective developmental robotics as a part of cognitive developmental robotics focusing on the affective aspects. This is followed by a review and discussion on several approaches for two focused aspects of affective developmental robotics. Finally, future issues involved in the development of a more authentic form of artificial empathy are discussed.

  14. Artificial Enzymes, "Chemzymes"

    DEFF Research Database (Denmark)

    Bjerre, Jeannette; Rousseau, Cyril Andre Raphaël; Pedersen, Lavinia Georgeta M


    Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models that successf......Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models...... that successfully perform Michaelis-Menten catalysis under enzymatic conditions (i.e., aqueous medium, neutral pH, ambient temperature) and for those that do, very high rate accelerations are seldomly seen. This review will provide a brief summary of the recent developments in artificial enzymes, so called...... "Chemzymes", based on cyclodextrins and other molecules. Only the chemzymes that have shown enzyme-like activity that has been quantified by different methods will be mentioned. This review will summarize the work done in the field of artificial glycosidases, oxidases, epoxidases, and esterases, as well...

  15. Creating an Artificial Muscle (United States)

    Bohon, Katherine; Krause, Sonja


    Striated skeletal muscle responds to a nerve impulse in less than 100 ms. In the past, polymeric gels and conducting polymers have been investigated for use as artificial muscle. However, the main problem with these materials is their relatively slow response (>3 seconds). On the other hand, electrorheological (ER) fluids are materials that change from a liquid to a solid upon application of an electric field. These fluids have a response on the order of a millisecond. A novel approach to artificial muscle utilizing the fast time response of ER fluids and the elasticity of polymeric gels has been investigated. A commercial sample of a two-part poly(dimethyl siloxane) (PDMS) dielectric gel was used. The PDMS was cured around two flexible electrodes 5 mm apart while a mixture of PDMS with solvent was cured between the electrodes. The solvents were either silicone oil or an ER fluid composed of crosslinked poly(ethylene oxide) (PEO) particles in silicone oil. The mixtures investigated were 90/10, 60/40, 50/50, 40/60, 10/90 PDMS/solvent. Upon application of a 6.2 kV/cm DC electric field the gel was reversibly compressed. The time response of the gel was actuator has been created using the 60/40 PDMS/ER fluid mixture.

  16. 鲁中南退化砂石山地人工幼林草本群落特征与物种多样性%Herbaceous Community Characteristics and Species Diversity of Young Artificial Forest of Degraded Granite Hilly Areas in Central-south of Shandong Province

    Institute of Scientific and Technical Information of China (English)

    邵水仙; 董智; 李红丽; 许婷婷; 张钦敬; 朱超


    为评价不同造林模式对鲁中南退化砂石山地林下草本植被的恢复效果,以该区域4种造林模式人工幼林为研究对象,运用样方调查与室内分析相结合的方法,研究了不同造林模式2011年、2013年林下草本群落数量特征及其多样性变化。结果表明:1)造林有助于林下草本植物的恢复、生长与发育,不同造林模式人工幼林林下草本种数、群落平均盖度、平均高度和平均密度均高于对照,且各指标均呈现混交造林模式高于纯林造林模式;除各模式草本种数变化不一致外,其余指标均呈现2013年高于2011年的趋势。2)造林可以改变林下草本植物的重要值和优势地位。不同造林模式的草本植物的主要优势种基本相同,造林2年和4年时,物种的动态变化明显,群落物种重要值与优势地位发生更替,造林4年后,群落主要优势种优势地位更加明显。3)不同造林模式的多样性指数高于对照,且呈现阔阔混交>针阔混交>纯林模式的趋势,多样性指数随造林时间的延长而呈下降趋势。%Different afforestation modes could produce significant influences on the survival rate,afforestation quality and even the development of plantation,especially in the area where the site conditions are poor.Such as in the central-south of Shandong province,as one of the ecological fragile regions of Shandong,the vegeta-tions scarcity,soil and water loss,land degradation and biodiversity decline are severe ecological problems and afforestation is difficult.In order to assess the restoration effect of different afforestation modes on herbaceous vegetation in degraded granite mountain in central-south of Shandong province,we took 4 young forests which were afforested in different modes as the study objects in this area,combined the sampling investigation and la-boratory analysis as our research method and studied the undergrowth herbaceous

  17. PEM fuel cell degradation

    Energy Technology Data Exchange (ETDEWEB)

    Borup, Rodney L [Los Alamos National Laboratory; Mukundan, Rangachary [Los Alamos National Laboratory


    The durability of PEM fuel cells is a major barrier to the commercialization of these systems for stationary and transportation power applications. While significant progress has been made in understanding degradation mechanisms and improving materials, further improvements in durability are required to meet commercialization targets. Catalyst and electrode durability remains a primary degradation mode, with much work reported on understanding how the catalyst and electrode structure degrades. Accelerated Stress Tests (ASTs) are used to rapidly evaluate component degradation, however the results are sometimes easy, and other times difficult to correlate. Tests that were developed to accelerate degradation of single components are shown to also affect other component's degradation modes. Non-ideal examples of this include ASTs examining catalyst degradation performances losses due to catalyst degradation do not always well correlate with catalyst surface area and also lead to losses in mass transport.

  18. Generative Artificial Intelligence : Philosophy and Theory of Artificial Intelligence

    NARCIS (Netherlands)

    van der Zant, Tijn; Kouw, Matthijs; Schomaker, Lambertus; Mueller, Vincent C.


    The closed systems of contemporary Artificial Intelligence do not seem to lead to intelligent machines in the near future. What is needed are open-ended systems with non-linear properties in order to create interesting properties for the scaffolding of an artificial mind. Using post-structuralistic

  19. Generative Artificial Intelligence : Philosophy and Theory of Artificial Intelligence

    NARCIS (Netherlands)

    van der Zant, Tijn; Kouw, Matthijs; Schomaker, Lambertus; Mueller, Vincent C.


    The closed systems of contemporary Artificial Intelligence do not seem to lead to intelligent machines in the near future. What is needed are open-ended systems with non-linear properties in order to create interesting properties for the scaffolding of an artificial mind. Using post-structuralistic

  20. Microbial identification by immunohybridization assay of artificial RNA labels (United States)

    Kourentzi, Katerina D.; Fox, George E.; Willson, Richard C.


    Ribosomal RNA (rRNA) and engineered stable artificial RNAs (aRNAs) are frequently used to monitor bacteria in complex ecosystems. In this work, we describe a solid-phase immunocapture hybridization assay that can be used with low molecular weight RNA targets. A biotinylated DNA probe is efficiently hybridized in solution with the target RNA, and the DNA-RNA hybrids are captured on streptavidin-coated plates and quantified using a DNA-RNA heteroduplex-specific antibody conjugated to alkaline phosphatase. The assay was shown to be specific for both 5S rRNA and low molecular weight (LMW) artificial RNAs and highly sensitive, allowing detection of as little as 5.2 ng (0.15 pmol) in the case of 5S rRNA. Target RNAs were readily detected even in the presence of excess nontarget RNA. Detection using DNA probes as small as 17 bases targeting a repetitive artificial RNA sequence in an engineered RNA was more efficient than the detection of a unique sequence.

  1. Mechanisms of humic substances degradation by fungi (United States)

    Chen, Y.; Hadar, Y.; Grinhut, T.


    Humic substances (HS) are formed by secondary synthesis reactions (humification) during the decay process and transformation of biomolecules originating from plants and other dead organisms. In nature, HS are extremely resistant to biological degradation. Thus, these substances are major components in the C cycle and in the biosphere and therefore, the understanding of the process leading to their formation and transformation and degradation is vital. Fungi active in the decomposition process of HS include mainly ascomycetes and basidiomycetes that are common in the upper layer of forest and grassland soils. Many basidiomycetes belong to the white-rot fungi (WRF) and litter-decomposing fungi (LDF). These fungi are considered to be the most efficient lignin degraders due to their nonspecific oxidizing enzymes: manganese peroxidase (MnP), lignin peroxidase (LiP) and laccase. Although bacteria dominate compost and participate in the turnover of HS, their ability to degrade stable macromolecules such as lignin and HS is limited. The overall objectives of this research were to corroborate biodegradation processes of HS by WRF. The specific objectives were: (i) To isolate, identify and characterize HS degrading WRF from biosolids (BS) compost; (ii) To study the biodegradation process of three types of HS, which differ in their structure, by WRF isolated from BS compost; and (iii) To investigate the mechanisms of HA degradation by WRF using two main approaches: (a) Study the physical and chemical analyses of the organic compounds obtained from direct fungal degradation of HA as well as elucidation of the relevant enzymatic reactions; and (b) Study the enzymatic and biochemical mechanisms involved during HA degradation. In order to study the capability of fungi to degrade HS, seventy fungal strains were isolated from biosolids (BS) compost. Two of the most active fungal species were identified based on rDNA sequences and designated Trametes sp. M23 and Phanerochaetesp., Y6

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

    Energy Technology Data Exchange (ETDEWEB)

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


    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

  3. Marketing places: multipurpose artificial reefs as tourist attraction proposal

    Directory of Open Access Journals (Sweden)

    Marco Antonio Moraes Ocke


    Full Text Available Marketing places focuses on the use of marketing activities as a way to leverage the socioeconomic development of cities, states and countries and in this context, the attractions of a given locality are essential to the growth of tourism in the region. From the literature review of concepts and types of attractions, this paper aims to suggest the convergence of the concepts of natural attraction and artificial attraction applied to artificial multipurpose artificial reefs and describe its hybrid nature to recover degraded areas by coastal erosion, increased marine biodiversity and the ability to improve the quality of waves for surfing, resulting in an increase of tourist flow of the region. Through the observation of cases in countries that have invested in the implementation of multipurpose artificial reefs it has been found positive results regarding tourism development and socioeconomic in these regions and thus, this paper considers the possibility of deployment of multipurpose artificial reefs along the Brazilian coast as a proposal to attract visitors and promote benefits to the receiving place.

  4. Distribuição sazonal de Culex (Culex eduardoi Casal & Garcia (Diptera, Culicidae em criadouros antrópicos introduzidos em mata residual degradada, área urbana de Curitiba, Paraná,Brasil Seazonal distribution of Culex (Culex eduardoi Casal & Garcia (Diptera, Culicidae in artificial receptacles in disturbed patch of forest degraded inurban area of Curitiba, Paraná, Brazil

    Directory of Open Access Journals (Sweden)

    Magda Clara Vieira da Costa Ribeiro


    Full Text Available The utilization of artificial receptacles to oviposition by mosquitoes in forest environment may indicate a sinantropic tendency or behaviour. Our data revealed that tires were as the most acceptable breeding for Culex (Culex eduardoi Casal & Garcia 1968.The population density of this species was higher and summer seasons.

  5. Susceptibility of anthocyanins to ex vivo degradation in human saliva (United States)

    Kamonpatana, Kom; Giusti, M. Mónica; Chitchumroonchokchai, Chureeporn; MorenoCruz, Maria; Riedl, Ken M.; Kumar, Purnima; Failla, Mark L.


    Some fruits and their anthocyanin-rich extracts have been reported to exhibit chemopreventive activity in the oral cavity. Insights regarding oral metabolism of anthocyanins remain limited. Anthocyanin-rich extracts from blueberry, chokeberry, black raspberry, red grape, and strawberry were incubated ex vivo with human saliva from 14 healthy subjects. All anthocyanins were partially degraded in saliva. Degradation of chokeberry anthocyanins in saliva was temperature dependent and decreased by heating saliva to 80 °C and after removal of cells. Glycosides of delphinidin and petunidin were more susceptible to degradation than those of cyanidin, pelargonidin, peonidin and malvidin in both intact and artificial saliva. Stability of di- and tri-saccharide conjugates of anthocyanidins slightly, but significantly, exceeded that of monosaccharide compounds. Ex vivo degradation of anthocyanins in saliva was significantly decreased after oral rinsing with antibacterial chlorhexidine. These results suggest that anthocyanin degradation in the mouth is structure-dependent and largely mediated by oral microbiota. PMID:22868153

  6. Microbial Aspects of Anaerobic BTEX Degradation

    Institute of Scientific and Technical Information of China (English)


    Combined with conventional methods, developments in both geochemical (delineation of redox processes) and molecular microbial methods (analysis of 16S rDNA genes and functional genes) have allowed us to study in details microorganisms and genes involved in the anaerobic degradation of benzene, toluene, ethylbenzene and xylene (BTEX) under specific redox conditions. This review summarizes recent research in this field. The potential for anaerobic BTEX degradation is widely spread. Specific groups of microorganisms appear to be involved in degradation under different redox conditions. Members of the Azoarcus/Thauera cluster perform BTEX degradation under denitrifying conditions, Geobacteraceae under Fe (III) reducing conditions and Desulfobacteriaceae under sulfate reducing conditions. The information so far obtained on biochemistry and molecular genetics of BTEX degradation indicates that each BTEX compound is funneled into the central benzyol-CoA pathway by a different peripheral pathway. The peripheral pathways of per BTEX compound show similarities among different physiological groups of microorganisms. We also describe how knowledge obtained on the microbial aspects of BTEX degradation can be used to enhance and monitor anaerobic BTEX degradation.

  7. Induction of genomic instability and activation of autophagy in artificial human aneuploid cells

    Energy Technology Data Exchange (ETDEWEB)

    Ariyoshi, Kentaro [Hirosaki University, Institute of Radiation Emergency Medicine, 66-1 Hon-cho, Hirosaki 036-8564 (Japan); Miura, Tomisato; Kasai, Kosuke; Fujishima, Yohei [Department of Biomedical Sciences, Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki 036-8564 (Japan); Oshimura, Mitsuo [Chromosome Engineering Research Center (CERC), Tottori University, Nishicho 86, Yonago, Tottori 683-8503 (Japan); Yoshida, Mitsuaki A., E-mail: [Hirosaki University, Institute of Radiation Emergency Medicine, 66-1 Hon-cho, Hirosaki 036-8564 (Japan)


    Highlights: • Clones with artificial aneuploidy of chromosome 8 or chromosome 22 both show inhibited proliferation and genomic instability. • Increased autophagy was observed in the artificially aneuploid clones. • Inhibition of autophagy resulted in increased genomic instability and DNA damage. • Intracellular levels of reactive oxygen species were up-regulated in the artificially aneuploid clones. - Abstract: Chromosome missegregation can lead to a change in chromosome number known as aneuploidy. Although aneuploidy is a known hallmark of cancer cells, the various mechanisms by which altered gene and/or DNA copy number facilitate tumorigenesis remain unclear. To understand the effect of aneuploidy occurring in non-tumorigenic human breast epithelial cells, we generated clones harboring artificial aneuploidy using microcell-mediated chromosome transfer. Our results demonstrate that clones with artificial aneuploidy of chromosome 8 or chromosome 22 both show inhibited proliferation and genomic instability. Also, the increased autophagy was observed in the artificially aneuploidy clones, and inhibition of autophagy resulted in increased genomic instability and DNA damage. In addition, the intracellular levels of reactive oxygen species were up-regulated in the artificially aneuploid clones, and inhibition of autophagy further increased the production of reactive oxygen species. Together, these results suggest that even a single extraneous chromosome can induce genomic instability, and that autophagy triggered by aneuploidy-induced stress is a mechanism to protect cells bearing abnormal chromosome number.

  8. Artificial Diets for Mosquitoes

    Directory of Open Access Journals (Sweden)

    Kristina K. Gonzales


    Full Text Available Mosquito-borne diseases are responsible for more than a million human deaths every year. Modern mosquito control strategies such as sterile insect technique (SIT, release of insects carrying a dominant lethal (RIDL, population replacement strategies (PR, and Wolbachia-based strategies require the rearing of large numbers of mosquitoes in culture for continuous release over an extended period of time. Anautogenous mosquitoes require essential nutrients for egg production, which they obtain through the acquisition and digestion of a protein-rich blood meal. Therefore, mosquito mass production in laboratories and other facilities relies on vertebrate blood from live animal hosts. However, vertebrate blood is expensive to acquire and hard to store for longer times especially under field conditions. This review discusses older and recent studies that were aimed at the development of artificial diets for mosquitoes in order to replace vertebrate blood.

  9. Artificial Immune Systems (2010)

    CERN Document Server

    Greensmith, Julie; Aickelin, Uwe


    The human immune system has numerous properties that make it ripe for exploitation in the computational domain, such as robustness and fault tolerance, and many different algorithms, collectively termed Artificial Immune Systems (AIS), have been inspired by it. Two generations of AIS are currently in use, with the first generation relying on simplified immune models and the second generation utilising interdisciplinary collaboration to develop a deeper understanding of the immune system and hence produce more complex models. Both generations of algorithms have been successfully applied to a variety of problems, including anomaly detection, pattern recognition, optimisation and robotics. In this chapter an overview of AIS is presented, its evolution is discussed, and it is shown that the diversification of the field is linked to the diversity of the immune system itself, leading to a number of algorithms as opposed to one archetypal system. Two case studies are also presented to help provide insight into the m...

  10. Generalized Adaptive Artificial Neural Networks (United States)

    Tawel, Raoul


    Mathematical model of supervised learning by artificial neural network provides for simultaneous adjustments of both temperatures of neurons and synaptic weights, and includes feedback as well as feedforward synaptic connections. Extension of mathematical model described in "Adaptive Neurons For Artificial Neural Networks" (NPO-17803). Dynamics of neural network represented in new model by less-restrictive continuous formalism.

  11. A Primer on Artificial Intelligence. (United States)

    Leal, Ralph A.

    A survey of literature on recent advances in the field of artificial intelligence provides a comprehensive introduction to this field for the non-technical reader. Important areas covered are: (1) definitions, (2) the brain and thinking, (3) heuristic search, and (4) programing languages used in the research of artificial intelligence. Some…

  12. Instructional Applications of Artificial Intelligence. (United States)

    Halff, Henry M.


    Surveys artificial intelligence and the development of computer-based tutors and speculates on the future of artificial intelligence in education. Includes discussion of the definitions of knowledge, expert systems (computer systems that solve tough technical problems), intelligent tutoring systems (ITS), and specific ITSs such as GUIDON, MYCIN,…

  13. Sucrose compared with artificial sweeteners

    DEFF Research Database (Denmark)

    Sørensen, Lone Brinkmann; Vasilaras, Tatjana H; Astrup, Arne


    There is a lack of appetite studies in free-living subjects supplying the habitual diet with either sucrose or artificially sweetened beverages and foods. Furthermore, the focus of artificial sweeteners has only been on the energy intake (EI) side of the energy-balance equation. The data are from...

  14. Artificial Ligaments: Promise or Panacea? (United States)

    Lubell, Adele


    The Food and Drug Administration has approved a prosthetic ligament for limited use in persons with damaged anterior cruciate ligaments (ACL). This article addresses ligament repair, ACL tears, current treatment, development of the Gore-Tex artificial ligament, other artificial ligaments in process, and arguments for and against their use.…

  15. Phylogenetic assessment of a new cypermethrin- degrading bacterium Gordonia sp.D2 based on 16S rDNA, gyrB and GyrB sequences%一株氯氰菊酯降解菌16S rDNA,gyrB和GyrB的系统发育分析

    Institute of Scientific and Technical Information of China (English)

    张久刚; 闫艳春


    A cypermethrin - degrading bacterium named as Gordonia sp. D2 was isolated from activated sludge of a wastewater treatment biore-actor. At 30 ℃ and pH 7.0, the removal rate of 100 mg cypennethrin L-1 was approximately 52.3% in mineral salts medium within 7.5 days, and extra carbon source addition could enhance the biodegradation. The isolate was identified as Gordonia genus through physio - bio- chemical identification combined with the phylogenetic analyses based on 16S rRNA, gyrB nucleotide and GyrB amino acid sequences. 16S rRNA sequences of strain D2 showed the highest similarity to G. amicalis DSM44461 and G. hydrophobica DSM44015T, with the same value of 98.1% ,meanwhile, D2 shows the highest similarity to G. hydrophobica JCA10086 with the value of 86.8% and 91.1% based on gyrB and GyrB. Three phylogenetic dendrograms were made, and results showed that 16S rRNA gene is suit for identifying the isolate to the genus level, gyrB gene and GyrB amino acid sequences are more adapted for phylogenetic analysis.%从农药厂污水处理池中分离得到一株氯氰菊酯降解菌,在30℃,pH 7.0的条件下,无机盐培养基中100mg/L的氯氰菊酯,经过7.5天,能够降解大约52.3%,外加碳源能够明显提高其降解性能.生理生化实验结合16S rDNA,gyrB和GyrB的系统发育分析,将其归为Gordonia菌属.在16S rDNA水平上,其与G.amicalis DSM44461和G.hydrophobica DSM44015的相似值最高,为98.1%;而在gyrB和GyrB水平上,其与G.hydrophobica JCM10086的相似值最高,分别为86.8%和91.1%.通过对所构建的系统发育树进行评估,表明16S rDNA序列适用于将分离菌株鉴定到属的水平上,而gyrB和GyrB更适用于在属内种的水平上进行系统发育的分析.

  16. Artificial insemination in marsupials. (United States)

    Rodger, John C; Paris, Damien B B P; Czarny, Natasha A; Harris, Merrilee S; Molinia, Frank C; Taggart, David A; Allen, Camryn D; Johnston, Stephen D


    Assisted breeding technology (ART), including artificial insemination (AI), has the potential to advance the conservation and welfare of marsupials. Many of the challenges facing AI and ART for marsupials are shared with other wild species. However, the marsupial mode of reproduction and development also poses unique challenges and opportunities. For the vast majority of marsupials, there is a dearth of knowledge regarding basic reproductive biology to guide an AI strategy. For threatened or endangered species, only the most basic reproductive information is available in most cases, if at all. Artificial insemination has been used to produce viable young in two marsupial species, the koala and tammar wallaby. However, in these species the timing of ovulation can be predicted with considerably more confidence than in any other marsupial. In a limited number of other marsupials, such precise timing of ovulation has only been achieved using hormonal treatment leading to conception but not live young. A unique marsupial ART strategy which has been shown to have promise is cross-fostering; the transfer of pouch young of a threatened species to the pouches of foster mothers of a common related species as a means to increase productivity. For the foreseeable future, except for a few highly iconic or well studied species, there is unlikely to be sufficient reproductive information on which to base AI. However, if more generic approaches can be developed; such as ICSI (to generate embryos) and female synchronization (to provide oocyte donors or embryo recipients), then the prospects for broader application of AI/ART to marsupials are promising.

  17. DNA from keratinous tissue

    DEFF Research Database (Denmark)

    Bengtsson, Camilla F.; Olsen, Maja E.; Brandt, Luise Ørsted


    Keratinous tissues such as nail, hair, horn, scales and feather have been used as a source of DNA for over 20 years. Particular benefits of such tissues include the ease with which they can be sampled, the relative stability of DNA in such tissues once sampled, and, in the context of ancient...... genetic analyses, the fact that sampling generally causes minimal visual damage to valuable specimens. Even when freshly sampled, however, the DNA quantity and quality in the fully keratinized parts of such tissues is extremely poor in comparison to other tissues such as blood and muscle – although little...... systematic research has been undertaken to characterize how such degradation may relate to sample source. In this review paper we present the current understanding of the quality and limitations of DNA in two key keratinous tissues, nail and hair. The findings indicate that although some fragments of nuclear...

  18. Isolation of oxygenase genes for indigo-forming activity from an artificially polluted soil metagenome by functional screening using Pseudomonas putida strains as hosts. (United States)

    Nagayama, Hirofumi; Sugawara, Tomonori; Endo, Ryo; Ono, Akira; Kato, Hiromi; Ohtsubo, Yoshiyuki; Nagata, Yuji; Tsuda, Masataka


    Metagenomes contain the DNA from many microorganisms, both culturable and non-culturable, and are a potential resource of novel genes. In this study, a 5.2-Gb metagenomic DNA library was constructed from a soil sample (artificially polluted with four aromatic compounds, i.e., biphenyl, phenanthrene, carbazole, and 3-chlorobenzoate) in Escherichia coli by using a broad-host-range cosmid vector. The resultant library was introduced into naphthalene-degrading Pseudomonas putida-derived strains having deficiencies in their naphthalene dioxygenase components, and indigo-forming clones on the indole-containing agar plates were screened. Cosmids isolated from 29 positive clones were classified by their various properties (original screening hosts, hosts showing indigo-forming activity, and digestion patterns with restriction enzymes), and six representative cosmids were chosen. Sequencing and in vitro transposon mutagenesis of the six cosmids resulted in the identification of genes encoding putative class B and D flavoprotein monooxygenases, a multicomponent hydroxylase, and a reductase that were responsible for the indigo-forming activity in the host cells. Among them, the genes encoding the multicomponent hydroxylase were demonstrated to be involved in phenol degradation. Furthermore, two genes encoding ring-cleavage dioxygenases were also found adjacent to the genes responsible for the indigo formation, and their functions were experimentally confirmed.

  19. Beyond AI: Artificial Dreams Conference

    CERN Document Server

    Zackova, Eva; Kelemen, Jozef; Beyond Artificial Intelligence : The Disappearing Human-Machine Divide


    This book is an edited collection of chapters based on the papers presented at the conference “Beyond AI: Artificial Dreams” held in Pilsen in November 2012. The aim of the conference was to question deep-rooted ideas of artificial intelligence and cast critical reflection on methods standing at its foundations.  Artificial Dreams epitomize our controversial quest for non-biological intelligence, and therefore the contributors of this book tried to fully exploit such a controversy in their respective chapters, which resulted in an interdisciplinary dialogue between experts from engineering, natural sciences and humanities.   While pursuing the Artificial Dreams, it has become clear that it is still more and more difficult to draw a clear divide between human and machine. And therefore this book tries to portrait such an image of what lies beyond artificial intelligence: we can see the disappearing human-machine divide, a very important phenomenon of nowadays technological society, the phenomenon which i...

  20. Conservative smoothing versus artificial viscosity

    Energy Technology Data Exchange (ETDEWEB)

    Guenther, C.; Hicks, D.L. [Michigan Technological Univ., Houghton, MI (United States); Swegle, J.W. [Sandia National Labs., Albuquerque, NM (United States). Solid and Structural Mechanics Dept.


    This report was stimulated by some recent investigations of S.P.H. (Smoothed Particle Hydrodynamics method). Solid dynamics computations with S.P.H. show symptoms of instabilities which are not eliminated by artificial viscosities. Both analysis and experiment indicate that conservative smoothing eliminates the instabilities in S.P.H. computations which artificial viscosities cannot. Questions were raised as to whether conservative smoothing might smear solutions more than artificial viscosity. Conservative smoothing, properly used, can produce more accurate solutions than the von Neumann-Richtmyer-Landshoff artificial viscosity which has been the standard for many years. The authors illustrate this using the vNR scheme on a test problem with known exact solution involving a shock collision in an ideal gas. They show that the norms of the errors with conservative smoothing are significantly smaller than the norms of the errors with artificial viscosity.

  1. Soft computing in artificial intelligence

    CERN Document Server

    Matson, Eric


    This book explores the concept of artificial intelligence based on knowledge-based algorithms. Given the current hardware and software technologies and artificial intelligence theories, we can think of how efficient to provide a solution, how best to implement a model and how successful to achieve it. This edition provides readers with the most recent progress and novel solutions in artificial intelligence. This book aims at presenting the research results and solutions of applications in relevance with artificial intelligence technologies. We propose to researchers and practitioners some methods to advance the intelligent systems and apply artificial intelligence to specific or general purpose. This book consists of 13 contributions that feature fuzzy (r, s)-minimal pre- and β-open sets, handling big coocurrence matrices, Xie-Beni-type fuzzy cluster validation, fuzzy c-regression models, combination of genetic algorithm and ant colony optimization, building expert system, fuzzy logic and neural network, ind...

  2. Degradation of microbial polyesters. (United States)

    Tokiwa, Yutaka; Calabia, Buenaventurada P


    Microbial polyhydroxyalkanoates (PHAs), one of the largest groups of thermoplastic polyesters are receiving much attention as biodegradable substitutes for non-degradable plastics. Poly(D-3-hydroxybutyrate) (PHB) is the most ubiquitous and most intensively studied PHA. Microorganisms degrading these polyesters are widely distributed in various environments. Although various PHB-degrading microorganisms and PHB depolymerases have been studied and characterized, there are still many groups of microorganisms and enzymes with varying properties awaiting various applications. Distributions of PHB-degrading microorganisms, factors affecting the biodegradability of PHB, and microbial and enzymatic degradation of PHB are discussed in this review. We also propose an application of a new isolated, thermophilic PHB-degrading microorganism, Streptomyces strain MG, for producing pure monomers of PHA and useful chemicals, including D-3-hydroxycarboxylic acids such as D-3-hydroxybutyric acid, by enzymatic degradation of PHB.

  3. What Is a Total Artificial Heart? (United States)

    ... the NHLBI on Twitter. What Is a Total Artificial Heart? A total artificial heart (TAH) is a device ... outside power source. Normal Heart and CardioWest Total Artificial Heart Figure A shows the normal structure and location ...

  4. Oligomerization and DNA-binding capacity of Pmr, a histone-like protein H1 (H-NS) family protein encoded on IncP-7 carbazole-degradative plasmid pCAR1. (United States)

    Suzuki, Chiho; Yun, Choong-Soo; Umeda, Takashi; Terabayashi, Tsuguno; Watanabe, Kazuya; Yamane, Hisakazu; Nojiri, Hideaki


    Pmr, a histone-like protein H1 (H-NS) family protein encoded on plasmid pCAR1, is a key factor in optimizing gene transcription on both pCAR1 and the host chromosome. To clarify the mode of function of Pmr, we performed gel filtration chromatography analysis and protein-protein cross-linking, and found that Pmr forms homo-oligomers, consisting of its homodimers. We also found, by atomic force microscopy, that Pmr has DNA-bridging capacity. From these results, Pmr was deduced to have features common to H-NS family proteins. Additionally, evaluating protein-DNA affinity is important to clarify the mode of function of Pmr, and hence we performed an electrophoretic mobility shift assay. Though Pmr formed high-order protein-DNA complexes and did not show preference for nucleic acid sequences, the C-terminal region of Pmr did, suggesting that the DNA-binding affinity of Pmr can be evaluated by using its C-terminal region.

  5. The artificial leaf. (United States)

    Nocera, Daniel G


    To convert the energy of sunlight into chemical energy, the leaf splits water via the photosynthetic process to produce molecular oxygen and hydrogen, which is in a form of separated protons and electrons. The primary steps of natural photosynthesis involve the absorption of sunlight and its conversion into spatially separated electron-hole pairs. The holes of this wireless current are captured by the oxygen evolving complex (OEC) of photosystem II (PSII) to oxidize water to oxygen. The electrons and protons produced as a byproduct of the OEC reaction are captured by ferrodoxin of photosystem I. With the aid of ferrodoxin-NADP(+) reductase, they are used to produce hydrogen in the form of NADPH. For a synthetic material to realize the solar energy conversion function of the leaf, the light-absorbing material must capture a solar photon to generate a wireless current that is harnessed by catalysts, which drive the four electron/hole fuel-forming water-splitting reaction under benign conditions and under 1 sun (100 mW/cm(2)) illumination. This Account describes the construction of an artificial leaf comprising earth-abundant elements by interfacing a triple junction, amorphous silicon photovoltaic with hydrogen- and oxygen-evolving catalysts made from a ternary alloy (NiMoZn) and a cobalt-phosphate cluster (Co-OEC), respectively. The latter captures the structural and functional attributes of the PSII-OEC. Similar to the PSII-OEC, the Co-OEC self-assembles upon oxidation of an earth-abundant metal ion from 2+ to 3+, may operate in natural water at room temperature, and is self-healing. The Co-OEC also activates H(2)O by a proton-coupled electron transfer mechanism in which the Co-OEC is increased by four hole equivalents akin to the S-state pumping of the Kok cycle of PSII. X-ray absorption spectroscopy studies have established that the Co-OEC is a structural relative of Mn(3)CaO(4)-Mn cubane of the PSII-OEC, where Co replaces Mn and the cubane is extended in a


    African Journals Online (AJOL)

    VOLTAGE COMPENSATION USING ARTIFICIAL NEURAL NETWORK: A CASE STUDY OF RUMUOLA DISTRIBUTION NETWORK. ... The artificial neural networks controller engaged to controlling the dynamic voltage ... Article Metrics.

  7. [Research and development of artificial retina material]. (United States)

    Hu, Ning; Yang, Jun; Peng, Chenglin; Wang, Xing; Zhang, Sijie; Zhang, Ying; Zheng, Erxin


    The application of artificial retina was introduced. The principal characteristics of artificial retina material were reviewed in particular. Moreover, the recent research development and application prospect were discussed.

  8. natural or artificial diets

    Directory of Open Access Journals (Sweden)

    A. O. Meyer-Willerer


    Full Text Available Se probaron alimentos artificiales y naturales con larva de camarón (Litopenaeus vannamei cultivados en diferentes recipientes. Estos fueron ocho frascos cónicos con 15L, ocho acuarios con 50L y como grupo control, seis tanques de fibra de vidrio con 1500L; todos con agua marina fresca y filtrada. La densidad inicial en todos los recipientes fue de 70 nauplios/L. Aquellos en frascos y acuarios recibieron ya sea dieta natural o artificial. El grupo control fue cultivado con dieta natural en los tanques grandes que utilizan los laboratorios para la producción masiva de postlarvas. El principal producto de excreción de larva de camarón es el ión amonio, que es tóxico cuando está presente en concentraciones elevadas. Se determinó diariamente con el método colorimétrico del indofenol. Los resultados muestran diferencias en la concentración del ión amonio y en la sobrevivencia de larvas entre las diferentes dietas y también entre los diferentes recipientes. En aquellos con volúmenes pequeños comparados con los grandes, se presentó mayor concentración de amonio (500 a 750µg/L, en aquellos con dietas naturales, debido a que este ión sirve de fertilizante a las algas adicionadas, necesitando efectuar recambios diarios de agua posteriores al noveno día de cultivo para mantener este ión a una concentración subletal. Se obtuvo una baja cosecha de postlarvas (menor a 15% con el alimento artificial larvario, debido a la presencia de protozoarios, alimentándose con el producto comercial precipitado en el fondo de los frascos o acuarios. Los acuarios con larvas alimentadas con dieta natural también mostraron concentraciones subletales de amonio al noveno día; sin embargo, la sobrevivencia fue cuatro veces mayor que con dietas artificiales. Los tanques control con dietas naturales presentaron tasas de sobrevivencia (70 ± 5% similares a la reportada por otros laboratorios.

  9. Bioengineering of Artificial Lymphoid Organs. (United States)

    Nosenko, M A; Drutskaya, M S; Moisenovich, M M; Nedospasov, S A


    This review addresses the issue of bioengineering of artificial lymphoid organs.Progress in this field may help to better understand the nature of the structure-function relations that exist in immune organs. Artifical lymphoid organs may also be advantageous in the therapy or correction of immunodefficiencies, autoimmune diseases, and cancer. The structural organization, development, and function of lymphoid tissue are analyzed with a focus on the role of intercellular contacts and on the cytokine signaling pathways regulating these processes. We describe various polymeric materials, as scaffolds, for artificial tissue engineering. Finally, published studies in which artificial lymphoid organs were generated are reviewed and possible future directions in the field are discussed.

  10. Artificial Neural Network Analysis System (United States)


    Contract No. DASG60-00-M-0201 Purchase request no.: Foot in the Door-01 Title Name: Artificial Neural Network Analysis System Company: Atlantic... Artificial Neural Network Analysis System 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Powell, Bruce C 5d. PROJECT NUMBER 5e. TASK NUMBER...34) 27-02-2001 Report Type N/A Dates Covered (from... to) ("DD MON YYYY") 28-10-2000 27-02-2001 Title and Subtitle Artificial Neural Network Analysis

  11. Artificial intelligence in medicine. (United States)

    Hamet, Pavel; Tremblay, Johanne


    Artificial Intelligence (AI) is a general term that implies the use of a computer to model intelligent behavior with minimal human intervention. AI is generally accepted as having started with the invention of robots. The term derives from the Czech word robota, meaning biosynthetic machines used as forced labor. In this field, Leonardo Da Vinci's lasting heritage is today's burgeoning use of robotic-assisted surgery, named after him, for complex urologic and gynecologic procedures. Da Vinci's sketchbooks of robots helped set the stage for this innovation. AI, described as the science and engineering of making intelligent machines, was officially born in 1956. The term is applicable to a broad range of items in medicine such as robotics, medical diagnosis, medical statistics, and human biology-up to and including today's "omics". AI in medicine, which is the focus of this review, has two main branches: virtual and physical. The virtual branch includes informatics approaches from deep learning information management to control of health management systems, including electronic health records, and active guidance of physicians in their treatment decisions. The physical branch is best represented by robots used to assist the elderly patient or the attending surgeon. Also embodied in this branch are targeted nanorobots, a unique new drug delivery system. The societal and ethical complexities of these applications require further reflection, proof of their medical utility, economic value, and development of interdisciplinary strategies for their wider application.

  12. Artificial Immune Systems Tutorial

    CERN Document Server

    Aickelin, Uwe


    The biological immune system is a robust, complex, adaptive system that defends the body from foreign pathogens. It is able to categorize all cells (or molecules) within the body as self-cells or non-self cells. It does this with the help of a distributed task force that has the intelligence to take action from a local and also a global perspective using its network of chemical messengers for communication. There are two major branches of the immune system. The innate immune system is an unchanging mechanism that detects and destroys certain invading organisms, whilst the adaptive immune system responds to previously unknown foreign cells and builds a response to them that can remain in the body over a long period of time. This remarkable information processing biological system has caught the attention of computer science in recent years. A novel computational intelligence technique, inspired by immunology, has emerged, called Artificial Immune Systems. Several concepts from the immune have been extracted an...

  13. Artificial Immune Systems

    CERN Document Server

    Aickelin, Uwe


    The biological immune system is a robust, complex, adaptive system that defends the body from foreign pathogens. It is able to categorize all cells (or molecules) within the body as self-cells or non-self cells. It does this with the help of a distributed task force that has the intelligence to take action from a local and also a global perspective using its network of chemical messengers for communication. There are two major branches of the immune system. The innate immune system is an unchanging mechanism that detects and destroys certain invading organisms, whilst the adaptive immune system responds to previously unknown foreign cells and builds a response to them that can remain in the body over a long period of time. This remarkable information processing biological system has caught the attention of computer science in recent years. A novel computational intelligence technique, inspired by immunology, has emerged, called Artificial Immune Systems. Several concepts from the immune have been extracted an...

  14. Programmable artificial phototactic microswimmer (United States)

    Dai, Baohu; Wang, Jizhuang; Xiong, Ze; Zhan, Xiaojun; Dai, Wei; Li, Chien-Cheng; Feng, Shien-Ping; Tang, Jinyao


    Phototaxis is commonly observed in motile photosynthetic microorganisms. For example, green algae are capable of swimming towards a light source (positive phototaxis) to receive more energy for photosynthesis, or away from a light source (negative phototaxis) to avoid radiation damage or to hide from predators. Recently, with the aim of applying nanoscale machinery to biomedical applications, various inorganic nanomotors based on different propulsion mechanisms have been demonstrated. The only method to control the direction of motion of these self-propelled micro/nanomotors is to incorporate a ferromagnetic material into their structure and use an external magnetic field for steering. Here, we show an artificial microswimmer that can sense and orient to the illumination direction of an external light source. Our microswimmer is a Janus nanotree containing a nanostructured photocathode and photoanode at opposite ends that release cations and anions, respectively, propelling the microswimmer by self-electrophoresis. Using chemical modifications, we can control the zeta potential of the photoanode and program the microswimmer to exhibit either positive or negative phototaxis. Finally, we show that a school of microswimmers mimics the collective phototactic behaviour of green algae in solution.

  15. BioArtificial polymers (United States)

    Szałata, Kamila; Gumi, Tania


    Nowadays, the polymer science has impact in practically all life areas. Countless benefits coming from the usage of materials with high mechanical and chemical resistance, variety of functionalities and potentiality of modification drive to the development of new application fields. Novel approaches of combining these synthetic substances with biomolecules lead to obtain multifunctional hybrid conjugates which merge the bioactivity of natural component with outstanding properties of artificial polymer. Over the decades, an immense progress in bioartificial composites domain allowed to reach a high level of knowledge in terms of natural-like systems engineering, leading to diverse strategies of biomolecule immobilization. Together with different available options, including covalent and noncovalent attachment, come various challenges, related mainly with maintaining the biological activity of fixed molecules. Even though the amount of applications that achieve commercial status is still not substantial, and is expanding continuously in the disciplines like "smart materials," biosensors, delivery systems, nanoreactors and many others. A huge number of remarkable developments reported in the literature present a potential of bioartificial conjugates as a fabrics with highly controllable structure and multiple functionalities, serving as a powerful nanotechnological tool. This novel approach brings closer biologists, chemists and engineers, who sharing their effort and complementing the knowledge can revolutionize the field of bioartificial polymer science.

  16. 转基因大豆内外源DNA在少孢根霉发酵中的降解%Degradation of endogenous and exogenous DNA in transgenic roundup ready soybean during fermentation with Rhizopus oligosporus

    Institute of Scientific and Technical Information of China (English)

    杨爱萍; 蒋义武; 祝长青; 何健; 刘欣; 宋尚新


    试验旨在研究转基因大豆内、外源基因在少孢根霉发酵过程中的降解变化规律,并探讨其降解规律与相关酶活性的关系.试验采用定性和定量PCR检测各基因的降解变化,同时测定相关酶活.结果表明:内源基因Lectin和外源基因EPSPS在高温蒸煮下降解至800 bp以下,在发酵4d后降解至200 bp以下;发酵过程中外源基因相对含量的变化与核酸酶、脂肪酶、蛋白酶活性的变化相一致.该研究为我国转基因食品加工过程中外源基因的降解及其机理研究提供一定的理论基础.%The purpose of study was to study the degradation of endogenous and exogenous genes and the relationship with associated enzymes activities in the process of fermentation with Rhizopus oligosporus. Qualitative and quantitative PCR were used to analyze the changes of the endogenous and exogenous gene, and the associated enzyme activities were also detected. The results showed that the endogenous gene Lectin and the exogenous gene EPSPS were degraded to less than 800 bp after high-temperature boiling and to less than 200 bp after four days of fermentation. In the process of fermentation, the variation of the relative content of exogenous genes was consistent with the variation of activities of associated nuclease, lipase and protease in soybeans. Therefore, this study provided theoretical foundations for the mechanism of exogenous gene degradation during the transgenic food processing.

  17. Bacterial Degradation of Pesticides

    DEFF Research Database (Denmark)

    Knudsen, Berith Elkær

    . Bioaugmentation i.e. addition of specific degrader organisms, has been suggested as an environmentally friendly and economically competitive strategy for cleaning polluted sites. Several organisms have been isolated, capable of degrading different compounds. However the capacity to degrade the desired compound...... SRS2, Variovorax SRS16 and Arthrobacter globiformis D47. The degradation capacity of each strain individually as well as two- and three-member consortia was studied in a sand column set up. Glass beads were added to the set up to create a dry patch, separating the organisms and the diuron-spiked sand...

  18. Darwin, artificial selection, and poverty. (United States)

    Sanchez, Luis


    This paper argues that the processes of evolutionary selection are becoming increasingly artificial, a trend that goes against the belief in a purely natural selection process claimed by Darwin's natural selection theory. Artificial selection is mentioned by Darwin, but it was ignored by Social Darwinists, and it is all but absent in neo-Darwinian thinking. This omission results in an underestimation of probable impacts of artificial selection upon assumed evolutionary processes, and has implications for the ideological uses of Darwin's language, particularly in relation to poverty and other social inequalities. The influence of artificial selection on genotypic and phenotypic adaptations arguably represents a substantial shift in the presumed path of evolution, a shift laden with both biological and political implications.

  19. Food analysis using artificial senses. (United States)

    Śliwińska, Magdalena; Wiśniewska, Paulina; Dymerski, Tomasz; Namieśnik, Jacek; Wardencki, Waldemar


    Nowadays, consumers are paying great attention to the characteristics of food such as smell, taste, and appearance. This motivates scientists to imitate human senses using devices known as electronic senses. These include electronic noses, electronic tongues, and computer vision. Thanks to the utilization of various sensors and methods of signal analysis, artificial senses are widely applied in food analysis for process monitoring and determining the quality and authenticity of foods. This paper summarizes achievements in the field of artificial senses. It includes a brief history of these systems, descriptions of most commonly used sensors (conductometric, potentiometric, amperometic/voltammetric, impedimetric, colorimetric, piezoelectric), data analysis methods (for example, artificial neural network (ANN), principal component analysis (PCA), model CIE L*a*b*), and application of artificial senses to food analysis, in particular quality control, authenticity and falsification assessment, and monitoring of production processes.

  20. Artificial intelligence: Deep neural reasoning (United States)

    Jaeger, Herbert


    The human brain can solve highly abstract reasoning problems using a neural network that is entirely physical. The underlying mechanisms are only partially understood, but an artificial network provides valuable insight. See Article p.471

  1. Fuel-Powered Artificial Muscles

    National Research Council Canada - National Science Library

    Von Howard Ebron; Zhiwei Yang; Daniel J. Seyer; Mikhail E. Kozlov; Jiyoung Oh; Hui Xie; Joselito Razal; Lee J. Hall; John P. Ferraris; Alan G. MacDiarmid; Ray H. Baughman


    ... long inactivity during battery recharge. To help solve these problems, we demonstrated two types of artificial muscles that convert the chemical energy of high-energy-density fuels to mechanical energy...

  2. Artificial Intelligence in Civil Engineering

    Directory of Open Access Journals (Sweden)

    Pengzhen Lu


    Full Text Available Artificial intelligence is a branch of computer science, involved in the research, design, and application of intelligent computer. Traditional methods for modeling and optimizing complex structure systems require huge amounts of computing resources, and artificial-intelligence-based solutions can often provide valuable alternatives for efficiently solving problems in the civil engineering. This paper summarizes recently developed methods and theories in the developing direction for applications of artificial intelligence in civil engineering, including evolutionary computation, neural networks, fuzzy systems, expert system, reasoning, classification, and learning, as well as others like chaos theory, cuckoo search, firefly algorithm, knowledge-based engineering, and simulated annealing. The main research trends are also pointed out in the end. The paper provides an overview of the advances of artificial intelligence applied in civil engineering.

  3. Experimental reconstruction of cervical esophageal defect with artificial esophagus made of polyurethane in a dog model. (United States)

    Jiang, H; Cui, Y; Ma, K; Gong, M; Chang, D; Wang, T


    The defect of esophagus after surgical excision in patients is usually replaced by autologous stomach, jejunum, or colon. The operation brings severe trauma and complications. Using artificial esophagus to replace the defect in situ can reduce the operative trauma, simplify the operative procedures, and decrease the influence to digestive function. A variety of experiments have been designed for developing a practical artificial esophagus. Nevertheless, a safe and reliable artificial esophagus is not yet available. The objective is to evaluate the possibility of the artificial esophagus made of non-degradable polyurethane materials being used in reconstruction of the segmental defect of cervical esophagus in beagles, observe the regeneration of esophageal tissue, and gather experience for future study. The cervical esophageal defects in 13 beagles were designed to 2-cm long and were constructed by the artificial esophagus made of non-degradable polyurethane materials. Nutrition supports were given after the operation. The operative mortality, anastomotic leakage, migration of artificial esophagus, and dysphagia were followed up. The regeneration of the esophageal tissues was evaluated by histopathology and immunohistochemical labeled streptavidin-biotin method. The surgical procedures were successfully completed in all beagles, and 12-month follow-ups were done. Only one beagle died of severe infection, and all others survived until being killed. The anastomotic leakage occurred in nine beagles, most of them (8/9) were cured after supportive therapy. The migration of artificial esophagus occurred in all 12 surviving beagles, and one artificial esophagus stayed in situ after migration. All 12 surviving beagles showed dysphagia with taking only fluid or soft food. No beagle died of malnutrition. The neo-esophagus was composed of granulation tissue, and the inner surface was covered by epithelium in 2-3 months completely. But the inner surface of neo-esophagus with

  4. Volatile hydrocarbons inhibit methanogenic crude oil degradation

    Directory of Open Access Journals (Sweden)

    Angela eSherry


    Full Text Available Methanogenic degradation of crude oil in subsurface sediments occurs slowly, but without the need for exogenous electron acceptors, is sustained for long periods and has enormous economic and environmental consequences. Here we show that volatile hydrocarbons are inhibitory to methanogenic oil biodegradation by comparing degradation of an artificially weathered crude oil with volatile hydrocarbons removed, with the same oil that was not weathered. Volatile hydrocarbons (nC5-nC10, methylcyclohexane, benzene, toluene and xylenes were quantified in the headspace of microcosms. Aliphatic (n-alkanes nC12-nC34 and aromatic hydrocarbons (4-methylbiphenyl, 3-methylbiphenyl, 2-methylnaphthalene, 1-methylnaphthalene were quantified in the total hydrocarbon fraction extracted from the microcosms. 16S rRNA genes from key microorganisms known to play an important role in methanogenic alkane degradation (Smithella and Methanomicrobiales were quantified by quantitative PCR. Methane production from degradation of weathered oil in microcosms was rapid (1.1 ± 0.1 µmol CH4/g sediment/day with stoichiometric yields consistent with degradation of heavier n-alkanes (nC12-nC34. For non-weathered oil, degradation rates in microcosms were significantly lower (0.4 ± 0.3 µmol CH4/g sediment/day. This indicated that volatile hydrocarbons present in the non-weathered oil inhibit, but do not completely halt, methanogenic alkane biodegradation. These findings are significant with respect to rates of biodegradation of crude oils with abundant volatile hydrocarbons in anoxic, sulphate-depleted subsurface environments, such as contaminated marine sediments which have been entrained below the sulfate-reduction zone, as well as crude oil biodegradation in petroleum reservoirs and contaminated aquifers.

  5. Medical applications of artificial intelligence

    CERN Document Server

    Agah, Arvin


    Enhanced, more reliable, and better understood than in the past, artificial intelligence (AI) systems can make providing healthcare more accurate, affordable, accessible, consistent, and efficient. However, AI technologies have not been as well integrated into medicine as predicted. In order to succeed, medical and computational scientists must develop hybrid systems that can effectively and efficiently integrate the experience of medical care professionals with capabilities of AI systems. After providing a general overview of artificial intelligence concepts, tools, and techniques, Medical Ap

  6. What are artificial neural networks?

    DEFF Research Database (Denmark)

    Krogh, Anders


    Artificial neural networks have been applied to problems ranging from speech recognition to prediction of protein secondary structure, classification of cancers and gene prediction. How do they work and what might they be good for? Udgivelsesdato: 2008-Feb......Artificial neural networks have been applied to problems ranging from speech recognition to prediction of protein secondary structure, classification of cancers and gene prediction. How do they work and what might they be good for? Udgivelsesdato: 2008-Feb...

  7. The handbook of artificial intelligence

    CERN Document Server

    Barr, Avron


    The Handbook of Artificial Intelligence, Volume II focuses on the improvements in artificial intelligence (AI) and its increasing applications, including programming languages, intelligent CAI systems, and the employment of AI in medicine, science, and education. The book first elaborates on programming languages for AI research and applications-oriented AI research. Discussions cover scientific applications, teiresias, applications in chemistry, dependencies and assumptions, AI programming-language features, and LISP. The manuscript then examines applications-oriented AI research in medicine

  8. The handbook of artificial intelligence

    CERN Document Server

    Barr, Avron J


    The Handbook of Artificial Intelligence, Volume I focuses on the progress in artificial intelligence (AI) and its increasing applications, including parsing, grammars, and search methods.The book first elaborates on AI, AI handbook and literature, problem representation, search methods, and sample search programs. The text then ponders on representation of knowledge, including survey of representation techniques and representation schemes. The manuscript explores understanding natural languages, as well as machine translation, grammars, parsing, test generation, and natural language processing

  9. Artificial weathering of granite

    Directory of Open Access Journals (Sweden)

    Silva Hermo, B.


    Full Text Available This article summarizes a series of artificial weathering tests run on granite designed to: simulate the action of weathering agents on buildings and identify the underlying mechanisms, determine the salt resistance of different types of rock; evaluate consolidation and water-repellent treatment durability; and confirm hypotheses about the origin of salts such as gypsum that are often found in granite buildings. Salt crystallization tests were also conducted, using sodium chloride, sodium sulphate, calcium sulphate and seawater solutions. One of these tests was conducted in a chamber specifically designed to simulate salt spray weathering and another in an SO2 chamber to ascertain whether granite is subject to sulphation. The test results are analyzed and discussed, along with the shortcomings of each type of trial as a method for simulating the decay observed in monuments. The effect of factors such as wet-dry conditions, type of saline solution and the position of the planes of weakness on the type of decay is also addressed.En este trabajo se hace una síntesis de varios ensayos de alteración artificial realizados con rocas graníticas. Estos ensayos tenían distintos objetivos: reproducir las formas de alteración encontradas en los edificios para llegar a conocer los mecanismos que las generan, determinar la resistencia de las diferentes rocas a la acción de las sales, evaluar la durabilidad de tratamientos de consolidación e hidrofugación y constatar hipótesis acerca del origen de algunas sales, como el yeso, que aparecen frecuentemente en edificios graníticos. En los ensayos de cristalización de sales se utilizaron disoluciones de cloruro de sodio, sulfato de sodio, sulfato de calcio y agua de mar. Uno de estos ensayos se llevó a cabo en una cámara especialmente diseñada para reproducir la alteración por aerosol marino y otro se realizó en una cámara de SO2, con el objeto de comprobar si en rocas graníticas se puede producir

  10. Phylogenetic and degradation characterization of Burkholderia cepacia WZ1 degrading herbicide quinclorac. (United States)

    Lü, Zhenmei; Min, Hang; Wu, Shuwen; Ruan, Aidong


    Strain WZI capable of degrading quinclorac was isolated from a pesticide manufactory soil and considered to be Burkholderia cepacia, belonged to bacteria, Proteobacteria, beta-Proteobacteria, based on morphology, physio-biochemical properties, whole cell fatty acid analysis and a partial sequencing of 16S rDNA. Strain WZ1 decomposed 90% of quinclorac at original concentration of 1000 mg L(-1) within 11 days. GC/MS analysis showed that the strain degraded quinclorac to 3,7-dichloro-8-quinoline and the cracked residue 2-chloro, 1,4-benzenedicarboxylic acid, indicating that the metabolic pathway was initiated by process of decarboxylation followed by cleavage of the aromatic ring. Stain WZ1 was also able to degrade some other herbicides and aromatic compounds, including 2,4,5-T, phenol, naphthalene and hydrochinone etc. This paper describes for the first time Phylogenetic and degradation characterization of a pure bacterium which, is able to mineralize quinclorac.

  11. Development of a totally implantable artificial larynx

    NARCIS (Netherlands)

    Verkerke, GJ; Veenstra, Aalze; de Vries, MP; Schutte, HK; Busscher, HJ; Herrmann, IF; Van der Mei, HC; Rakhorst, G; Clements, MP


    Background. The consequences of a life-saving laryngectomy are still very distressing. The Eureka project "Artificial Larynx" aims at realization of an implantable artificial larynx to eliminate all drawbacks. Methods. The artificial larynx will consist of artificial vocal folds of adjustable pitch

  12. Air Quality Forecasting through Different Statistical and Artificial Intelligence Techniques (United States)

    Mishra, D.; Goyal, P.


    Urban air pollution forecasting has emerged as an acute problem in recent years because there are sever environmental degradation due to increase in harmful air pollutants in the ambient atmosphere. In this study, there are different types of statistical as well as artificial intelligence techniques are used for forecasting and analysis of air pollution over Delhi urban area. These techniques are principle component analysis (PCA), multiple linear regression (MLR) and artificial neural network (ANN) and the forecasting are observed in good agreement with the observed concentrations through Central Pollution Control Board (CPCB) at different locations in Delhi. But such methods suffers from disadvantages like they provide limited accuracy as they are unable to predict the extreme points i.e. the pollution maximum and minimum cut-offs cannot be determined using such approach. Also, such methods are inefficient approach for better output forecasting. But with the advancement in technology and research, an alternative to the above traditional methods has been proposed i.e. the coupling of statistical techniques with artificial Intelligence (AI) can be used for forecasting purposes. The coupling of PCA, ANN and fuzzy logic is used for forecasting of air pollutant over Delhi urban area. The statistical measures e.g., correlation coefficient (R), normalized mean square error (NMSE), fractional bias (FB) and index of agreement (IOA) of the proposed model are observed in better agreement with the all other models. Hence, the coupling of statistical and artificial intelligence can be use for the forecasting of air pollutant over urban area.


    Directory of Open Access Journals (Sweden)

    B. Kristoffer Segerholm,


    Full Text Available Moisture sorption in wood-plastic composites (WPCs affects their durability and dimensional stability. In certain outdoor exposures, the moisture properties of WPCs are altered due to e.g. cracks induced by swelling and shrinkage of the components, as well as UV degradation or biological attack. The aim of this work was to study the effect of different artificial ageing routes on the moisture sorption properties of WPCs. Extruded WPCs were prepared with either unmodified or acetylated wood and recycled high-density polyethylene (HDPE. The WPC samples were artificially aged involving water soaking, artificial weathering, and white- or brown-rot decay in different combinations. After the ageing, the samples were conditioned in either 65% or 90% relative humidity (RH until equilibrium moisture content was reached. A dynamic moisture sorption analyzer was used to monitor the sorption rate of samples subjected to a climate change from 65% to 90% RH. Scanning electron microscopy was used to study the surface morphology of the aged composites. Results showed that the artificial weathering caused cracking of the HDPE matrix at the composite surface, as well as a wood-matrix debonding, resulting in an increased moisture sorption rate. The WPC samples subjected to white-rot decay showed the highest moisture sorption rate.

  14. Batteries: Imaging degradation (United States)

    Shearing, Paul R.


    The degradation and failure of Li-ion batteries is strongly associated with electrode microstructure change upon (de)lithiation. Now, an operando X-ray tomography approach is shown to correlate changes in the microstructure of electrodes to cell performance, and thereby predict degradation pathways.

  15. Syntrophy in Methanogenic Degradation

    NARCIS (Netherlands)

    Worm, P.; Müller, N.; Plugge, C.M.; Stams, A.J.M.; Schink, B.


    This chapter deals with microbial communities of bacteria and archaea that closely cooperate in methanogenic degradation and perform metabolic functions in this community that neither one of them could carry out alone. The methanogenic degradation of fatty acids, alcohols, most aromatic compounds, a

  16. Rate of NDF degradation

    DEFF Research Database (Denmark)

    Weisbjerg, Martin Riis; Koukolová, V; Lund, Peter


    Degradation profiles for NDF were estimated for 83 samples of grass/grass-clover, 27 samples of cereal whole crop and 14 samples of maize whole crop.......Degradation profiles for NDF were estimated for 83 samples of grass/grass-clover, 27 samples of cereal whole crop and 14 samples of maize whole crop....

  17. Degradation of aqueous solutions of camphor by heterogeneous photocatalysis. (United States)

    Sirtori, Carla; Altvater, Priscila K; de Freitas, Adriane M; Peralta-Zamora, Patricio G


    In this study the photocatalytic degradation of aqueous solutions of camphor was investigated by using TiO2 and ZnO photocatalysts. In the presence of artificial UV-light the highly photosensitive camphor was almost totally degraded after reaction times of 60 min. However, under these conditions the mineralization degree was lower than 25%. In the presence of semiconductors the degradation was complete after a treatment time of about 30 min. Moreover, the mineralization was considerably greater, mainly with the use of TiO2 (> 80% at reaction time of 60 min). Heterogeneous photocatalytic processes applied in the presence of solar radiation show a promising degradation capability. TiO2-based processes afforded mineralization degrees of about 90% after a reaction time of 120 min, when the system was assisted by aeration.

  18. [Application of the QIAamp DNA Investigator Kit and Prepfiler Forensic DNA Extraction Kit in genomic DNA extraction from skeletal remains]. (United States)

    Ludwikowska-Pawłowska, Małgorzata; Jacewicz, Renata; Jedrzejczyk, Maciej; Prośniak, Adam; Berent, Jarosław


    The report presents an application of the QIAamp DNA Investigator Kit and PrepFiler Forensic DNA Extraction Kit in genomic DNA extraction from post-mortem highly degraded skeletal remains. The analysis included 25 bone samples collected on autopsy. DNA extraction was performed in accordance with the QIAamp DNA Investigator Kit and PrepFiler Forensic DNA Extraction Kit manufacturer's isolation protocols. Amplification was performed on a Biometra termocycler using the AmpFISTR Identifiler PCR Amplification Kit according to the manufacturer's protocol. Typing of PCR products was carried out on an ABI Prism 377 DNA sequencer. The recommended parameters for GeneScan analysis and Genotyper software were followed. The authors demonstrated that the QIAamp DNA Investigator Kit was more effective, convenient and statistically significantly better method which may be employed in DNA extraction from bone specimens.

  19. Sex Determination from Fragmented and Degenerated DNA by Amplified Product-Length Polymorphism Bidirectional SNP Analysis of Amelogenin and SRY Genes. (United States)

    Masuyama, Kotoka; Shojo, Hideki; Nakanishi, Hiroaki; Inokuchi, Shota; Adachi, Noboru


    Sex determination is important in archeology and anthropology for the study of past societies, cultures, and human activities. Sex determination is also one of the most important components of individual identification in criminal investigations. We developed a new method of sex determination by detecting a single-nucleotide polymorphism in the amelogenin gene using amplified product-length polymorphisms in combination with sex-determining region Y analysis. We particularly focused on the most common types of postmortem DNA damage in ancient and forensic samples: fragmentation and nucleotide modification resulting from deamination. Amplicon size was designed to be less than 60 bp to make the method more useful for analyzing degraded DNA samples. All DNA samples collected from eight Japanese individuals (four male, four female) were evaluated correctly using our method. The detection limit for accurate sex determination was determined to be 20 pg of DNA. We compared our new method with commercial short tandem repeat analysis kits using DNA samples artificially fragmented by ultraviolet irradiation. Our novel method was the most robust for highly fragmented DNA samples. To deal with allelic dropout resulting from deamination, we adopted "bidirectional analysis," which analyzed samples from both sense and antisense strands. This new method was applied to 14 Jomon individuals (3500-year-old bone samples) whose sex had been identified morphologically. We could correctly identify the sex of 11 out of 14 individuals. These results show that our method is reliable for the sex determination of highly degenerated samples.

  20. Evaluating Ethanol-based Sample Preservation to Facilitate Use of DNA Barcoding in Routine Freshwater Biomonitoring Programs Using Benthic Macroinvertebrates (United States)

    Molecular methods, such as DNA barcoding, have the potential in enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biom...

  1. A mitochondrial DNA SNP multiplex assigning Caucasians into 36 haplo- and subhaplogroups

    DEFF Research Database (Denmark)

    Mikkelsen, Martin; Rockenbauer, Eszter; Sørensen, Erik;


    Mitochondrial DNA (mtDNA) is maternally inherited without recombination events and has a high copy number, which makes mtDNA analysis feasible even when genomic DNA is sparse or degraded. Here, we present a SNP typing assay with 33 previously described mtDNA coding region SNPs for haplogroup assi...

  2. Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system. (United States)

    Vilchez-Vargas, Ramiro; Geffers, Robert; Suárez-Diez, María; Conte, Ianina; Waliczek, Agnes; Kaser, Vanessa Sabrina; Kralova, Monika; Junca, Howard; Pieper, Dietmar H


    Despite various efforts to develop tools to detect and compare the catabolic potential and activity for pollutant degradation in environmental samples, there is still a need for an open-source, curated and reliable array method. We developed a custom array system including a novel normalization strategy that can be applied to any microarray design, allowing the calculation of the reliability of signals and make cross-experimental comparisons. Array probes, which are fully available to the scientific community, were designed from knowledge-based curated databases for key aromatic catabolic gene families and key alkane degradation genes. This design assigns signals to the respective protein subfamilies, thus directly inferring function and substrate specificity. Experimental procedures were optimized using DNA of four genome sequenced biodegradation strains and reliability of signals assessed through a novel normalization procedure, where a plasmid containing four artificial targets in increased copy numbers and co-amplified with the environmental DNA served as an internal calibration curve. The array system was applied to assess the catabolic gene landscape and transcriptome of aromatic contaminated environmental samples, confirming the abundance of catabolic gene subfamilies previously detected by functional metagenomics but also revealing the presence of previously undetected catabolic groups and specifically their expression under pollutant stress.

  3. Extracellular DNA: the tip of root defenses? (United States)

    Hawes, Martha C; Curlango-Rivera, Gilberto; Wen, Fushi; White, Gerard J; Vanetten, Hans D; Xiong, Zhongguo


    This review discusses how extracellular DNA (exDNA) might function in plant defense, and at what level(s) of innate immunity this process might operate. A new role for extracellular factors in mammalian defense has been described in a series of studies. These studies reveal that cells including neutrophils, eosinophils, and mast cells produce 'extracellular traps' (ETs) consisting of histone-linked exDNA. When pathogens are attracted to such ETs, they are trapped and killed. When the exDNA component of ETs is degraded, trapping is impaired and resistance against invasion is reduced. Conversely, mutation of microbial genes encoding exDNases that degrade exDNA results in loss of virulence. This discovery that exDNases are virulence factors opens new avenues for disease control. In plants, exDNA is required for defense of the root tip. Innate immunity-related proteins are among a group of >100 proteins secreted from the root cap and root border cell populations. Direct tests revealed that exDNA also is rapidly synthesized and exported from the root tip. When this exDNA is degraded by the endonuclease DNase 1, root tip resistance to fungal infection is lost; when the polymeric structure is degraded more slowly, by the exonuclease BAL31, loss of resistance to fungal infection is delayed accordingly. The results suggest that root border cells may function in a manner analogous to that which occurs in mammalian cells.

  4. Intermittent degradation and schizotypy

    Directory of Open Access Journals (Sweden)

    Matthew W. Roché


    Full Text Available Intermittent degradation refers to transient detrimental disruptions in task performance. This phenomenon has been repeatedly observed in the performance data of patients with schizophrenia. Whether intermittent degradation is a feature of the liability for schizophrenia (i.e., schizotypy is an open question. Further, the specificity of intermittent degradation to schizotypy has yet to be investigated. To address these questions, 92 undergraduate participants completed a battery of self-report questionnaires assessing schizotypy and psychological state variables (e.g., anxiety, depression, and their reaction times were recorded as they did so. Intermittent degradation was defined as the number of times a subject’s reaction time for questionnaire items met or exceeded three standard deviations from his or her mean reaction time after controlling for each item’s information processing load. Intermittent degradation scores were correlated with questionnaire scores. Our results indicate that intermittent degradation is associated with total scores on measures of positive and disorganized schizotypy, but unrelated to total scores on measures of negative schizotypy and psychological state variables. Intermittent degradation is interpreted as potentially derivative of schizotypy and a candidate endophenotypic marker worthy of continued research.

  5. Silk structure and degradation. (United States)

    Liu, Bin; Song, Yu-wei; Jin, Li; Wang, Zhi-jian; Pu, De-yong; Lin, Shao-qiang; Zhou, Chan; You, Hua-jian; Ma, Yan; Li, Jin-min; Yang, Li; Sung, K L Paul; Zhang, Yao-guang


    To investigate the structure of silk and its degradation properties, we have monitored the structure of silk using scanning electron microscopy and frozen sections. Raw silk and degummed raw silk were immersed in four types of degradation solutions for 156 d to observe their degradation properties. The subcutaneous implants in rats were removed after 7, 14, 56, 84, 129, and 145 d for frozen sectioning and subsequent staining with hematoxylin and eosin (H.E.), DAPI, Beta-actin and Collagen I immunofluorescence staining. The in vitro weight loss ratio of raw silk and degummed raw silk in water, PBS, DMEM and DMEM containing 10% FBS (F-DMEM) were, respectively, 14%/11%, 12.5%/12.9%, 11.1%/14.3%, 8.8%/11.6%. Silk began to degrade after 7 d subcutaneous implantation and after 145 d non-degraded silk was still observed. These findings suggest the immunogenicity of fibroin and sericin had no essential difference. In the process of in vitro degradation of silk, the role of the enzyme is not significant. The in vivo degradation of silk is related to phagocytotic activity and fibroblasts may be involved in this process to secrete collagen. This study also shows the developing process of cocoons and raw silk.

  6. Functional DNA-containing nanomaterials: cellular applications in biosensing, imaging, and targeted therapy. (United States)

    Liang, Hao; Zhang, Xiao-Bing; Lv, Yifan; Gong, Liang; Wang, Ruowen; Zhu, Xiaoyan; Yang, Ronghua; Tan, Weihong


    CONSPECTUS: DNA performs a vital function as a carrier of genetic code, but in the field of nanotechnology, DNA molecules can catalyze chemical reactions in the cell, that is, DNAzymes, or bind with target-specific ligands, that is, aptamers. These functional DNAs with different modifications have been developed for sensing, imaging, and therapeutic systems. Thus, functional DNAs hold great promise for future applications in nanotechnology and bioanalysis. However, these functional DNAs face challenges, especially in the field of biomedicine. For example, functional DNAs typically require the use of cationic transfection reagents to realize cellular uptake. Such reagents enter the cells, increasing the difficulty of performing bioassays in vivo and potentially damaging the cell's nucleus. To address this obstacle, nanomaterials, such as metallic, carbon, silica, or magnetic materials, have been utilized as DNA carriers or assistants. In this Account, we describe selected examples of functional DNA-containing nanomaterials and their applications from our recent research and those of others. As models, we have chosen to highlight DNA/nanomaterial complexes consisting of gold nanoparticles, graphene oxides, and aptamer-micelles, and we illustrate the potential of such complexes in biosensing, imaging, and medical diagnostics. Under proper conditions, multiple ligand-receptor interactions, decreased steric hindrance, and increased surface roughness can be achieved from a high density of DNA that is bound to the surface of nanomaterials, resulting in a higher affinity for complementary DNA and other targets. In addition, this high density of DNA causes a high local salt concentration and negative charge density, which can prevent DNA degradation. For example, DNAzymes assembled on gold nanoparticles can effectively catalyze chemical reactions even in living cells. And it has been confirmed that DNA-nanomaterial complexes can enter cells more easily than free single

  7. Artificial gametes from stem cells. (United States)

    Moreno, Inmaculada; Míguez-Forjan, Jose Manuel; Simón, Carlos


    The generation of artificial gametes is a real challenge for the scientific community today. In vitro development of human eggs and sperm will pave the way for the understanding of the complex process of human gametogenesis and will provide with human gametes for the study of infertility and the onset of some inherited disorders. However, the great promise of artificial gametes resides in their future application on reproductive treatments for all these people wishing to have genetically related children and for which gamete donation is now their unique option of parenthood. This is the case of infertile patients devoid of suitable gametes, same sex couples, singles and those fertile couples in a high risk of transmitting serious diseases to their progeny. In the search of the best method to obtain artificial gametes, many researchers have successfully obtained human germ cell-like cells from stem cells at different stages of differentiation. In the near future, this field will evolve to new methods providing not only viable but also functional and safe artificial germ cells. These artificial sperm and eggs should be able to recapitulate all the genetic and epigenetic processes needed for the correct gametogenesis, fertilization and embryogenesis leading to the birth of a healthy and fertile newborn.


    Institute of Scientific and Technical Information of China (English)

    Boubacar KANE; Pierre Y.JULIEN


    An extensive database of reservoir sedimentation surveys throughout continental United States is compiled and analyzed to determine specific degradation SD relationships as function of mean annual rainfall R, drainage area A, and watershed slope S. The database contains 1463 field measurements and specific degradation relationships are defined as function of A, R and S. Weak trends and significant variability in the data are noticeable. Specific degradation measurements are log normally distributed with respect to R, A, and S and 95% confidence intervals are determined accordingly. The accuracy of the predictions does not significantly increase as more independent variables are added to the regression analyses.

  9. An artificially generated atmosphere near a lunar base (United States)

    Burns, Jack O.; Fernini, Ilias; Sulkanen, Martin; Duric, Nebojsa; Taylor, G. Jeffrey; Johnson, Stewart W.


    We discuss the formation of an artificial atmosphere generated by vigorous lunar base activity in this paper. We developed an analytical, steady-state model for a lunar atmosphere based upon previous investigations of the Moon's atmosphere from Apollo. Constant gas-injection rates, ballistic trajectories, and a Maxwellian particle distribution for an oxygen-like gas are assumed. Even for the extreme case of continuous He-3 mining of the lunar regolith, we find that the lunar atmosphere would not significantly degrade astronomical observations beyond about 10 km from the mining operation.

  10. [Application and potential of genome engineering by artificial enzymes]. (United States)

    Nomura, Wataru


    Artificial zinc finger proteins (ZFPs) consist of Cys2-His2-type modules composed of approximately 30 amino acids that adopt a ββα structure and coordinate a zinc ion. ZFPs recognizing specific DNA target sequences can substitute for the binding domains of various DNA-modifying enzymes to create designer nucleases, recombinases, and methylases with programmable sequence specificity. Enzymatic genome editing and modification can be applied to many fields of basic research and medicine. The recent development of new platforms using transcription activator-like effector (TALE) proteins or the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has expanded the range of possibilities for genome-editing technologies. These technologies empower investigators with the ability to efficiently knockout or regulate the functions of genes of interest. In this review, we discuss historical advancements in artificial ZFP applications and important issues that may influence the future of genome editing and engineering technologies. The development of artificial ZFPs has greatly increased the feasibility of manipulating endogenous gene functions through transcriptional control and gene modification. Advances in the ZFP, TALE, and CRISPR/Cas platforms have paved the way for the next generation of genome engineering approaches. Perspectives for the future of genome engineering are also discussed, including applications of targeting specific genomic alleles and studies in synthetic biology.

  11. Artificial heart for humanoid robot (United States)

    Potnuru, Akshay; Wu, Lianjun; Tadesse, Yonas


    A soft robotic device inspired by the pumping action of a biological heart is presented in this study. Developing artificial heart to a humanoid robot enables us to make a better biomedical device for ultimate use in humans. As technology continues to become more advanced, the methods in which we implement high performance and biomimetic artificial organs is getting nearer each day. In this paper, we present the design and development of a soft artificial heart that can be used in a humanoid robot and simulate the functions of a human heart using shape memory alloy technology. The robotic heart is designed to pump a blood-like fluid to parts of the robot such as the face to simulate someone blushing or when someone is angry by the use of elastomeric substrates and certain features for the transport of fluids.

  12. Knitting and weaving artificial muscles (United States)

    Maziz, Ali; Concas, Alessandro; Khaldi, Alexandre; Stålhand, Jonas; Persson, Nils-Krister; Jager, Edwin W. H.


    A need exists for artificial muscles that are silent, soft, and compliant, with performance characteristics similar to those of skeletal muscle, enabling natural interaction of assistive devices with humans. By combining one of humankind’s oldest technologies, textile processing, with electroactive polymers, we demonstrate here the feasibility of wearable, soft artificial muscles made by weaving and knitting, with tunable force and strain. These textile actuators were produced from cellulose yarns assembled into fabrics and coated with conducting polymers using a metal-free deposition. To increase the output force, we assembled yarns in parallel by weaving. The force scaled linearly with the number of yarns in the woven fabric. To amplify the strain, we knitted a stretchable fabric, exhibiting a 53-fold increase in strain. In addition, the textile construction added mechanical stability to the actuators. Textile processing permits scalable and rational production of wearable artificial muscles, and enables novel ways to design assistive devices. PMID:28138542

  13. [Implantation of the artificial retina]. (United States)

    Yagi, T; Hayashida, Y


    In some degenerative retinal diseases, e.g., retinitis pigmentosa and age-related macular degeneration, the photoreceptors are destroyed to cause serious visual defects. Recent studies on blind human subjects revealed that a large number of ganglion cells remains intact and is capable of transmitting signals to the brain to evoke partial visual perception. This provided hope to compensate for the visual defects with retinal prostheses. The recent progress of microfabrication technique made it possible to implement the Vary Large Scale Integrated circuit, the artificial retina, which emulates a part of retinal function. The idea of implanting the artificial retina to the patients was proposed recently and experiments using animals have been put into practice. This article surveys the front line of the artificial retina implantation.

  14. Computational aerodynamics and artificial intelligence (United States)

    Mehta, U. B.; Kutler, P.


    The general principles of artificial intelligence are reviewed and speculations are made concerning how knowledge based systems can accelerate the process of acquiring new knowledge in aerodynamics, how computational fluid dynamics may use expert systems, and how expert systems may speed the design and development process. In addition, the anatomy of an idealized expert system called AERODYNAMICIST is discussed. Resource requirements for using artificial intelligence in computational fluid dynamics and aerodynamics are examined. Three main conclusions are presented. First, there are two related aspects of computational aerodynamics: reasoning and calculating. Second, a substantial portion of reasoning can be achieved with artificial intelligence. It offers the opportunity of using computers as reasoning machines to set the stage for efficient calculating. Third, expert systems are likely to be new assets of institutions involved in aeronautics for various tasks of computational aerodynamics.

  15. Artificial sweeteners: safe or unsafe? (United States)

    Qurrat-ul-Ain; Khan, Sohaib Ahmed


    Artificial sweeteners or intense sweeteners are sugar substitutes that are used as an alternative to table sugar. They are many times sweeter than natural sugar and as they contain no calories, they may be used to control weight and obesity. Extensive scientific research has demonstrated the safety of the six low-calorie sweeteners currently approved for use in foods in the U.S. and Europe (stevia, acesulfame-K, aspartame, neotame, saccharin and sucralose), if taken in acceptable quantities daily. There is some ongoing debate over whether artificial sweetener usage poses a health threat .This review article aims to cover thehealth benefits, and risks, of consuming artificial sweeteners, and discusses natural sweeteners which can be used as alternatives.

  16. Autophagy in DNA Damage Response

    Directory of Open Access Journals (Sweden)

    Piotr Czarny


    Full Text Available DNA damage response (DDR involves DNA repair, cell cycle regulation and apoptosis, but autophagy is also suggested to play a role in DDR. Autophagy can be activated in response to DNA-damaging agents, but the exact mechanism underlying this activation is not fully understood, although it is suggested that it involves the inhibition of mammalian target of rapamycin complex 1 (mTORC1. mTORC1 represses autophagy via phosphorylation of the ULK1/2–Atg13–FIP200 complex thus preventing maturation of pre-autophagosomal structures. When DNA damage occurs, it is recognized by some proteins or their complexes, such as poly(ADPribose polymerase 1 (PARP-1, Mre11–Rad50–Nbs1 (MRN complex or FOXO3, which activate repressors of mTORC1. SQSTM1/p62 is one of the proteins whose levels are regulated via autophagic degradation. Inhibition of autophagy by knockout of FIP200 results in upregulation of SQSTM1/p62, enhanced DNA damage and less efficient damage repair. Mitophagy, one form of autophagy involved in the selective degradation of mitochondria, may also play role in DDR. It degrades abnormal mitochondria and can either repress or activate apoptosis, but the exact mechanism remains unknown. There is a need to clarify the role of autophagy in DDR, as this process may possess several important biomedical applications, involving also cancer therapy.

  17. Thraustochytrid protists degrade hydrocarbons

    Digital Repository Service at National Institute of Oceanography (India)

    Raikar, M.T.; Raghukumar, S.; Vani, V.; David, J.J.; Chandramohan, D.

    Although thraustochytrid protists are known to be of widespread occurrence in the sea, their hydrocarbon-degrading abilities have never been investigated. We isolated thraustochytrids from coastal waters and sediments of Goa coast by enriching MPN...

  18. How do polymers degrade? (United States)

    Lyu, Suping


    Materials derived from agricultural products such as cellulose, starch, polylactide, etc. are more sustainable and environmentally benign than those derived from petroleum. However, applications of these polymers are limited by their processing properties, chemical and thermal stabilities. For example, polyethylene terephthalate fabrics last for many years under normal use conditions, but polylactide fabrics cannot due to chemical degradation. There are two primary mechanisms through which these polymers degrade: via hydrolysis and via oxidation. Both of these two mechanisms are related to combined factors such as monomer chemistry, chain configuration, chain mobility, crystallinity, and permeation to water and oxygen, and product geometry. In this talk, we will discuss how these materials degrade and how the degradation depends on these factors under application conditions. Both experimental studies and mathematical modeling will be presented.

  19. Degradation of implant materials

    CERN Document Server

    Eliaz, Noam


    This book surveys the degradation of implant materials, reviewing in detail such failure mechanisms as corrosion, fatigue and wear, along with monitoring techniques. Surveys common implant biomaterials, as well as procedures for implant retrieval and analysis.

  20. Environmental degradation in biocomposites

    CSIR Research Space (South Africa)

    John, Maya J


    Full Text Available molecular chain scission, surface oxidation, and breakdown of molecules to form active radicals. The main degradation processes occurring by weathering includes photoradiation, thermal degradation, photooxidation, and hydrolysis [22,23]. The effect... which exhibits transitions from glassy stage to a rubbery stage at its glass transition temperature. ● Weathering Composites commonly used in automotive and aerospace applications are subjected to varying conditions of sunlight, rain, moisture...

  1. Bacteria and lignin degradation

    Institute of Scientific and Technical Information of China (English)

    Jing LI; Hongli YUAN; Jinshui YANG


    Lignin is both the most abundant aromatic (phenolic) polymer and the second most abundant raw material.It is degraded and modified by bacteria in the natural world,and bacteria seem to play a leading role in decomposing lignin in aquatic ecosystems.Lignin-degrading bacteria approach the polymer by mechanisms such as tunneling,erosion,and cavitation.With the advantages of immense environmental adaptability and biochemical versatility,bacteria deserve to be studied for their ligninolytic potential.

  2. Fecundación artificial



    Por Fecundación artificial se entiende, la fecundación de una hembra sin el servicio directo del macho, es decir la introducción al aparato genital femenino, del esperma que se ha recogido por medios artificiales. Esta fecundación, practicada en debidas condiciones, tiene el mismo efecto de la fecundación natural, con las ventajas que veremos más adelante. La fecundación artificial permite explotar un reproductor a su máximum de capacidad, ya que se considera, para no hacer cálculo...

  3. Training Applications of Artificial Intelligence. (United States)


    nearifest tLer,sclvCs in ELO r operatii.L costs in the life C’VclE Of the ef’uijjteft. E F re\\ lously rcntione6 ey~ arrle of usingF the 1lirefineer...Ibid., p. 35. 4. Avron Barr and Edward Feigenbaum, The Handbook of Artificial Intelligence, Vol. 1, p. 2. 5. Wissam W. Ahmed, "Theories of Artificial...Barr, Avron and Geigenbaum, Edward A. ed. The Handbook of Arti- ficial Intelligence. Vol. 1. Stanford: heuristech Press. 1981. Gevartner, William B

  4. Rewritable artificial magnetic charge ice

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Y. -L.; Xiao, Z. -L.; Snezhko, A.; Xu, J.; Ocola, L. E.; Divan, R.; Pearson, J. E.; Crabtree, G. W.; Kwok, W. -K.


    Artificial ices enable the study of geometrical frustration by design and through direct observation. However, it has proven difficult to achieve tailored long-range ordering of their diverse configurations, limiting both fundamental and applied research directions. We designed an artificial spin structure that produces a magnetic charge ice with tunable long-range ordering of eight different configurations. We also developed a technique to precisely manipulate the local magnetic charge states and demonstrate write-read-erase multifunctionality at room temperature. This globally reconfigurable and locally writable magnetic charge ice could provide a setting for designing magnetic monopole defects, tailoring magnonics, and controlling the properties of other two-dimensional materials.

  5. Artificial intelligence techniques in Prolog

    CERN Document Server

    Shoham, Yoav


    Artificial Intelligence Techniques in Prolog introduces the reader to the use of well-established algorithmic techniques in the field of artificial intelligence (AI), with Prolog as the implementation language. The techniques considered cover general areas such as search, rule-based systems, and truth maintenance, as well as constraint satisfaction and uncertainty management. Specific application domains such as temporal reasoning, machine learning, and natural language are also discussed.Comprised of 10 chapters, this book begins with an overview of Prolog, paying particular attention to Prol

  6. Cutting the fat: artificial muscle oscillators for lighter, cheaper, and slimmer devices (United States)

    O'Brien, Benjamin M.; Rosset, Samuel; Shea, Herbert R.; Anderson, Iain A.


    Artificial muscles based on dielectric elastomers show enormous promise for a wide range of applications and are slowly moving from the lab to industry. One problem for industrial uptake is the expensive, rigid, heavy and bulky high voltage driver, sensor and control circuitry that artificial muscle devices currently require. One recent development, the Dielectric Elastomer Switch(es) (DES), shows promise for substantially reducing auxiliary circuitry and helping to mature the technology. DES are piezoresistive elements that can be used to form logic, driver, and sensor circuitry. One particularly useful feature of DES is their ability to embed oscillatory behaviour directly into an artificial muscle device. In this paper we will focus on how DES oscillators can break down the barriers to industrial adoption for artificial muscle devices. We have developed an improved artificial muscle ring oscillator and applied it to form a mechanosensitive conveyor. The free running oscillator ran at 4.4 Hz for 1056 cycles before failing due to electrode degradation. With better materials artificial muscle oscillators could open the door to robots with increased power to weight ratios, simple-to-control peristaltic pumps, and commercially viable artificial muscle motors.

  7. Modeling biodegradation and kinetics of glyphosate by artificial neural network. (United States)

    Nourouzi, Mohsen M; Chuah, Teong G; Choong, Thomas S Y; Rabiei, F


    An artificial neural network (ANN) model was developed to simulate the biodegradation of herbicide glyphosate [2-(Phosphonomethylamino) acetic acid] in a solution with varying parameters pH, inoculum size and initial glyphosate concentration. The predictive ability of ANN model was also compared with Monod model. The result showed that ANN model was able to accurately predict the experimental results. A low ratio of self-inhibition and half saturation constants of Haldane equations (glyphosate on bacteria growth. The value of K(i)/K(s) increased when the mixed inoculum size was increased from 10(4) to 10(6) bacteria/mL. It was found that the percentage of glyphosate degradation reached a maximum value of 99% at an optimum pH 6-7 while for pH values higher than 9 or lower than 4, no degradation was observed.

  8. Effects of Type I Collagen Degradation on the Durability of Three Adhesive Systems in the Early Phase of Dentin Bonding


    Lin Hu; Yu-hong Xiao; Ming Fang; Yu Gao; Li Huang; An-qi Jia; Ji-hua Chen


    Objective This study was designed to evaluate the effects of type I collagen degradation on the durability of three adhesive systems in the early phase of dentin bonding. Methods Bonded dentin specimens were prepared using three different types of adhesive systems. Micro-tensile bond strength and degradation of collagen were tested before, and after 1 month or 4 months of aging in artificial saliva. The relationship between micro-tensile bond strength and collagen degradation was analyzed by ...

  9. Polyanhydride degradation and erosion. (United States)

    Göpferich, A; Tessmar, J


    It was the intention of this paper to give a survey on the degradation and erosion of polyanhydrides. Due to the multitude of polymers that have been synthesized in this class of material in recent years, it was not possible to discuss all polyanhydrides that have gained in significance based on their application. It was rather the intention to provide a broad picture on polyanhydride degradation and erosion based on the knowledge that we have from those polymers that have been intensively investigated. To reach this goal this review contains several sections. First, the foundation for an understanding of the nomenclature are laid by defining degradation and erosion which was deemed necessary because many different definitions exist in the current literature. Next, the properties of major classes of anhydrides are reviewed and the impact of geometry on degradation and erosion is discussed. A complicated issue is the control of drug release from degradable polymers. Therefore, the aspect of erosion-controlled release and drug stability inside polyanhydrides are discussed. Towards the end of the paper models are briefly reviewed that describe the erosion of polyanhydrides. Empirical models as well as Monte-Carlo-based approaches are described. Finally it is outlined how theoretical models can help to answer the question why polyanhydrides are surface eroding. A look at the microstructure and the results from these models lead to the conclusion that polyanhydrides are surface eroding due to their fast degradation. However they switch to bulk erosion once the device dimensions drop below a critical limit.

  10. Microwave-induced inactivation of DNA-based hybrid catalyst in asymmetric catalysis. (United States)

    Zhao, Hua; Shen, Kai


    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.

  11. DNA damage in plant herbarium tissue.

    Directory of Open Access Journals (Sweden)

    Martijn Staats

    Full Text Available Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative assessment of DNA post-mortem damage is essential to determine the accuracy of molecular data from herbarium specimens. In this study we present an assessment of DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA. In addition, we assess DNA degradation as a result of strand breaks and other types of polymerase non-bypassable damage by quantitative real-time PCR. Comparing four pairs of fresh and herbarium specimens of the same individuals we quantitatively assess post-mortem DNA damage, directly after specimen preparation, as well as after long-term herbarium storage. After specimen preparation we estimate the proportion of gene copy numbers of plastid, mitochondrial, and nuclear DNA to be 2.4-3.8% of fresh control DNA and 1.0-1.3% after long-term herbarium storage, indicating that nearly all DNA damage occurs on specimen preparation. In addition, there is no evidence of preferential degradation of organelle versus nuclear genomes. Increased levels of C→T/G→A transitions were observed in old herbarium plastid DNA, representing 21.8% of observed miscoding lesions. We interpret this type of post-mortem DNA damage-derived modification to have arisen from the hydrolytic deamination of cytosine during long-term herbarium storage. Our results suggest that reliable sequence data can be obtained from herbarium specimens.

  12. DNA Damage in Plant Herbarium Tissue (United States)

    Staats, Martijn; Cuenca, Argelia; Richardson, James E.; Vrielink-van Ginkel, Ria; Petersen, Gitte; Seberg, Ole; Bakker, Freek T.


    Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative assessment of DNA post-mortem damage is essential to determine the accuracy of molecular data from herbarium specimens. In this study we present an assessment of DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA. In addition, we assess DNA degradation as a result of strand breaks and other types of polymerase non-bypassable damage by quantitative real-time PCR. Comparing four pairs of fresh and herbarium specimens of the same individuals we quantitatively assess post-mortem DNA damage, directly after specimen preparation, as well as after long-term herbarium storage. After specimen preparation we estimate the proportion of gene copy numbers of plastid, mitochondrial, and nuclear DNA to be 2.4–3.8% of fresh control DNA and 1.0–1.3% after long-term herbarium storage, indicating that nearly all DNA damage occurs on specimen preparation. In addition, there is no evidence of preferential degradation of organelle versus nuclear genomes. Increased levels of C→T/G→A transitions were observed in old herbarium plastid DNA, representing 21.8% of observed miscoding lesions. We interpret this type of post-mortem DNA damage-derived modification to have arisen from the hydrolytic deamination of cytosine during long-term herbarium storage. Our results suggest that reliable sequence data can be obtained from herbarium specimens. PMID:22163018

  13. DDE remediation and degradation. (United States)

    Thomas, John E; Ou, Li-Tse; All-Agely, Abid


    DDT and its metabolites, DDD and DDE, have been shown to be recalcitrant to degradation. The parent compound, DDT, was used extensively worldwide starting in 1939 and was banned in the United States in 1973. The daughter compound, DDE, may result from aerobic degradation, abiotic dehydrochlorination, or photochemical decomposition. DDE has also occurred as a contaminant in commercial-grade DDT. The p,p'-DDE isomer is more biologically active than the o,p-DDE, with a reported half-life of -5.7 years. However, when DDT was repeatedly applied to the soil, the DDE concentration may remain unchanged for more than 20 yr. Remediation of DDE-contaminated soil and water may be done by several techniques. Phytoremediation involves translocating DDT, DDD, and DDE from the soil into the plant, although some aquatic species (duckweed > elodea > parrot feather) can transform DDT into predominantly DDD with some DDE being formed. Of all the plants that can uptake DDE, Cucurbita pepo has been the most extensively studied, with translocation values approaching "hyperaccumulation" levels. Soil moisture, temperature, and plant density have all been documented as important factors in the uptake of DDE by Cucurbita pepo. Uptake may also be influenced positively by amendments such as biosurfactants, mycorrhizal inoculants, and low molecular weight organic acids (e.g., citric and oxalic acids). DDE microbial degradation by dehalogenases, dioxygenases, and hydrolases occurs under the proper conditions. Although several aerobic degradation pathways have been proposed, none has been fully verified. Very few aerobic pure cultures are capable of fully degrading DDE to CO2. Cometabolism of DDE by Pseudomonas sp., Alicaligens sp., and Terrabacter sp. grown on biphenyl has been reported; however, not all bacterial species that produce biphenyl dioxygenase degraded DDE. Arsenic and copper inhibit DDE degradation by aerobic microorganisms. Similarly, metal chelates such as EDTA inhibit the

  14. DNA Nanotechnology (United States)

    Taniguchi, Masateru; Kawai, Tomoji


    DNA is one candidate of promising molecules for molecular electronic devices, since it has the double helix structure with pi-electron bases for electron transport, the address at 0.4 nm intervals, and the self-assembly. Electrical conductivity and nanostructure of DNA and modified DNA molecules are investigated in order to research the application of DNA in nanoelectronic devices. It has been revealed that DNA is a wide-gap semiconductor in the absence of doping. The conductivity of DNA has been controlled by chemical doping, electric field doping, and photo-doping. It has found that Poly(dG)[middle dot]Poly(dC) has the best conductivity and can function as a conducting nanowire. The pattern of DNA network is controlled by changing the concentration of the DNA solution.

  15. Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double strand break ends


    Zhu, Zhu; Chung, Woo-Hyun; Shim, Eun Yong; Lee, Sang Eun; Ira, Grzegorz


    Formation of single-strand DNA (ssDNA) tails at a double-strand break (DSB) is a key step in homologous recombination and DNA damage signaling. The enzyme(s) producing ssDNA at DSBs in eukaryotes remains unknown. We monitored 5’-strand resection at inducible DSB ends and identified proteins required for two stages of resection: initiation and long-range 5’-strand resection. The Mre11-Rad50-Xrs2 complex (MRX) initiates 5’ degradation, whereas Sgs1 and Dna2 degrade 5’-strands exposing long 3’-s...

  16. DNA Methylation


    Alokail, Majed S.; Alenad, Amal M.


    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication e...

  17. Thinking, Creativity, and Artificial Intelligence. (United States)

    DeSiano, Michael; DeSiano, Salvatore

    This document provides an introduction to the relationship between the current knowledge of focused and creative thinking and artificial intelligence. A model for stages of focused and creative thinking gives: problem encounter/setting, preparation, concentration/incubation, clarification/generation and evaluation/judgment. While a computer can…

  18. Artificial Video for Video Analysis (United States)

    Gallis, Michael R.


    This paper discusses the use of video analysis software and computer-generated animations for student activities. The use of artificial video affords the opportunity for students to study phenomena for which a real video may not be easy or even possible to procure, using analysis software with which the students are already familiar. We will…

  19. Artificial Intelligence Assists Ultrasonic Inspection (United States)

    Schaefer, Lloyd A.; Willenberg, James D.


    Subtle indications of flaws extracted from ultrasonic waveforms. Ultrasonic-inspection system uses artificial intelligence to help in identification of hidden flaws in electron-beam-welded castings. System involves application of flaw-classification logic to analysis of ultrasonic waveforms.

  20. Artificial penile nodules: case reports.


    Lim, K B; Seow, C.S.; Tulip, T; Daniel, M.; Vijayasingham, S M


    An interesting cultural practice of implanting foreign bodies under the skin of the penis for enhancing sexual excitement in the man's sexual partner is described. Recognition of this is important to venereologists because of their primary concern with the genital area. The term artificial penile nodule has been suggested for the condition resulting from this practice.

  1. Artificial neural networks in medicine

    Energy Technology Data Exchange (ETDEWEB)

    Keller, P.E.


    This Technology Brief provides an overview of artificial neural networks (ANN). A definition and explanation of an ANN is given and situations in which an ANN is used are described. ANN applications to medicine specifically are then explored and the areas in which it is currently being used are discussed. Included are medical diagnostic aides, biochemical analysis, medical image analysis and drug development.

  2. Making Artificial Seawater More Natural

    Institute of Scientific and Technical Information of China (English)


    @@ Marine fish will die if placed in fresh water and they cannot live in simple salt water. Instead, they need water that contains a mixture of different ingredients, as found in natural seawater. Conventional methods of making artificial seawater have shortcomings, because the water so achieved is only composed of mineral elements and lacks organic components similar to those in natural seawater.

  3. Artificial Intelligence Assists Ultrasonic Inspection (United States)

    Schaefer, Lloyd A.; Willenberg, James D.


    Subtle indications of flaws extracted from ultrasonic waveforms. Ultrasonic-inspection system uses artificial intelligence to help in identification of hidden flaws in electron-beam-welded castings. System involves application of flaw-classification logic to analysis of ultrasonic waveforms.

  4. Yersinia enterocolitica-mediated degradation of neutrophil extracellular traps (NETs). (United States)

    Möllerherm, Helene; Neumann, Ariane; Schilcher, Katrin; Blodkamp, Stefanie; Zeitouni, Nathalie E; Dersch, Petra; Lüthje, Petra; Naim, Hassan Y; Zinkernagel, Annelies S; von Köckritz-Blickwede, Maren


    Neutrophil extracellular trap (NET) formation is described as a tool of the innate host defence to fight against invading pathogens. Fibre-like DNA structures associated with proteins such as histones, cell-specific enzymes and antimicrobial peptides are released, thereby entrapping invading pathogens. It has been reported that several bacteria are able to degrade NETs by nucleases and thus evade the NET-mediated entrapment. Here we studied the ability of three different Yersinia serotypes to induce and degrade NETs. We found that the common Yersinia enterocolitica serotypes O:3, O:8 and O:9 were able to induce NETs in human blood-derived neutrophils during the first hour of co-incubation. At later time points, the NET amount was reduced, suggesting that degradation of NETs has occurred. This was confirmed by NET degradation assays with phorbol-myristate-acetate-pre-stimulated neutrophils. In addition, we found that the Yersinia supernatants were able to degrade purified plasmid DNA. The absence of Ca(2+) and Mg(2+) ions, but not that of a protease inhibitor cocktail, completely abolished NET degradation. We therefore postulate that Y. enterocolitica produces Ca(2+)/Mg(2+)-dependent NET-degrading nucleases as shown for some Gram-positive pathogens.

  5. Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

    NARCIS (Netherlands)

    Hehir-Kwa, J.Y.; Egmont-Peterson, M.; Janssen, I.M.; Smeets, D.F.C.M.; Geurts van Kessel, A.H.M.; Veltman, J.A.


    Recently, comparative genomic hybridization onto bacterial artificial chromosome (BAC) arrays (array-based comparative genomic hybridization) has proved to be successful for the detection of submicroscopic DNA copy-number variations in health and disease. Technological improvements to achieve a

  6. "Artificial But Better Than Nothing". (United States)

    Blaschke, Sarah; O'Callaghan, Clare C; Schofield, Penelope


    To investigate patient, staff, and carer responses to an environmental intervention in an oncology clinic waiting room and evaluate the acceptability of artificial plant materials. Design Postintervention: Cross-sectional survey study. Oncology outpatient clinic waiting room located in a metropolitan comprehensive cancer center in Australia. Observer ratings of perceived qualities and effects of lifelike (fake) plants while spending time in the waiting room. Convenience sample ( N = 143) consisted of 73 cancer patients, 13 staff, 52 carers, and 5 "others" aged between 24 and 89 years ( M = 56, SD = 14.5). Artificial plant arrangements, hanging installations, two movable green walls, and one rock garden on wheels placed throughout the outpatients' clinic waiting room. Eighty-one percent (115/142) of respondents noticed the green features when first entering the waiting room and 67% (90/134) noticed they were artificial. Eighty-one percent (115/142) indicated "like/like a lot" when reporting their first reaction to the green features. Forty-eight percent (68/143) were positively affected and 23% (33/143) were very positively affected. Eighty-one percent (110/135) agreed/strongly agreed that "The greenery brightens the waiting room," 62% (80/130) agreed/strongly agreed that they "prefer living plants," and 76% (101/133) agreed/strongly agreed that "'lifelike' plants are better than no plants." Comments included mostly positive appraisals and occasional adverse reactions to artificial plants. No significant differences were found between patients', staff, and carers' reactions. The environmental intervention positively impacted patients', staff, and carers' perceptions of the oncology waiting room environment. Patients, staff, and carers mostly accepted artificial plants as an alternative design solution to real plants.

  7. Another Step Closer to Artificial Blood (United States)

    ... news/fullstory_162357.html Another Step Closer to Artificial Blood Synthetic product could save lives on battlefield and ... 5, 2016 SATURDAY, Dec. 3, 2016 (HealthDay News) -- Artificial blood stored as a powder could one day revolutionize ...

  8. 21 CFR 886.3200 - Artificial eye. (United States)


    ... OPHTHALMIC DEVICES Prosthetic Devices § 886.3200 Artificial eye. (a) Identification. An artificial eye is a... inserted in a patient's eye socket anterior to an orbital implant, or the eviscerated eyeball, for...

  9. Non-Nutritive Sweeters (Artificial Sweeteners) (United States)

    ... Workplace Food and Beverage Toolkit Non-Nutritive Sweeteners (Artificial Sweeteners) Updated:Mar 18,2014 Got a sweet tooth? Here’s the scoop on artificial sweeteners or “non-nutritive sweeteners” as we call them. ...

  10. Drift Degradation Analysis

    Energy Technology Data Exchange (ETDEWEB)

    D. Kicker


    Degradation of underground openings as a function of time is a natural and expected occurrence for any subsurface excavation. Over time, changes occur to both the stress condition and the strength of the rock mass due to several interacting factors. Once the factors contributing to degradation are characterized, the effects of drift degradation can typically be mitigated through appropriate design and maintenance of the ground support system. However, for the emplacement drifts of the geologic repository at Yucca Mountain, it is necessary to characterize drift degradation over a 10,000-year period, which is well beyond the functional period of the ground support system. This document provides an analysis of the amount of drift degradation anticipated in repository emplacement drifts for discrete events and time increments extending throughout the 10,000-year regulatory period for postclosure performance. This revision of the drift degradation analysis was developed to support the license application and fulfill specific agreement items between the U.S. Nuclear Regulatory Commission (NRC) and the U.S. Department of Energy (DOE). The earlier versions of ''Drift Degradation Analysis'' (BSC 2001 [DIRS 156304]) relied primarily on the DRKBA numerical code, which provides for a probabilistic key-block assessment based on realistic fracture patterns determined from field mapping in the Exploratory Studies Facility (ESF) at Yucca Mountain. A key block is defined as a critical block in the surrounding rock mass of an excavation, which is removable and oriented in an unsafe manner such that it is likely to move into an opening unless support is provided. However, the use of the DRKBA code to determine potential rockfall data at the repository horizon during the postclosure period has several limitations: (1) The DRKBA code cannot explicitly apply dynamic loads due to seismic ground motion. (2) The DRKBA code cannot explicitly apply loads due to thermal

  11. DNA-based assembly lines and nanofactories. (United States)

    Simmel, Friedrich C


    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.

  12. Microbial degradation of herbicides. (United States)

    Singh, Baljinder; Singh, Kashmir


    Herbicides remain the most effective, efficient and economical way to control weeds; and its market continues to grow even with the plethora of generic products. With the development of herbicide-tolerant crops, use of herbicides is increasing around the world that has resulted in severe contamination of the environment. The strategies are now being developed to clean these substances in an economical and eco-friendly manner. In this review, an attempt has been made to pool all the available literature on the biodegradation of key herbicides, clodinafop propargyl, 2,4-dichlorophenoxyacetic acid, atrazine, metolachlor, diuron, glyphosate, imazapyr, pendimethalin and paraquat under the following objectives: (1) to highlight the general characteristic and mode of action, (2) to enlist toxicity in animals, (3) to pool microorganisms capable of degrading herbicides, (4) to discuss the assessment of herbicides degradation by efficient microbes, (5) to highlight biodegradation pathways, (6) to discuss the molecular basis of degradation, (7) to enlist the products of herbicides under degradation process, (8) to highlight the factors effecting biodegradation of herbicides and (9) to discuss the future aspects of herbicides degradation. This review may be useful in developing safer and economic microbiological methods for cleanup of soil and water contaminated with such compounds.

  13. Dna Sequencing (United States)

    Tabor, Stanley; Richardson, Charles C.


    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  14. Introduction to Concepts in Artificial Neural Networks (United States)

    Niebur, Dagmar


    This introduction to artificial neural networks summarizes some basic concepts of computational neuroscience and the resulting models of artificial neurons. The terminology of biological and artificial neurons, biological and machine learning and neural processing is introduced. The concepts of supervised and unsupervised learning are explained with examples from the power system area. Finally, a taxonomy of different types of neurons and different classes of artificial neural networks is presented.

  15. Specific hydrolysis of DNA by Ce4+-ODN hybrid

    Institute of Scientific and Technical Information of China (English)

    SHEN; Hebai; ZHOU; Wenjun; YANG; Yongtao; ZHANG; Feng


    The cerium complex bound to the derivative of oligoDNA has been synthesized successfully that can hydrolyze DNA with sequence-specificity. The synthesized derivative of oligoDNA, 5′-EDTA-P-10 mers ODN, was demonstrated by HPLC. The fluorescence spectrum of Tb3+ was detected after its interaction with the hybrid of 10-mers ODN and 26-mers ODN and the results show that the artificial endo-enzyme can recognize and combine firmly with the substrate DNA. The electrophorogram shows that the cerium-oligoDNA hybrid can specifically hydrolyze its substrate DNA and the cleavage site of this hydrolysis reaction is also discussed. This artificial nuclease can be widely used in molecular biology and genetic engineering as one kind of endo-enzyme.

  16. Virus-Like Particles of mRNA with Artificial Minimal Coat Proteins

    NARCIS (Netherlands)

    Jekhmane, Shehrazade; Haas, De Rob; Paulino Da Silva Filho, Omar; Asbeck, van Alexander H.; Favretto, Marco Emanuele; Hernandez Garcia, Armando; Brock, Roland; Vries, De Renko


    RNA has enormous potential as a therapeutic, yet, the successful application depends on efficient delivery strategies. In this study, we demonstrate that a designed artificial viral coat protein, which self-assembles with DNA to form rod-shaped virus-like particles (VLPs), also encapsulates and

  17. Multicomponent synthesis of artificial nucleases and their RNase and DNase activity

    Directory of Open Access Journals (Sweden)

    Anton V. Gulevich


    Full Text Available The synthesis of new, artificial ribonucleases containing two amino acid residues connected by an aliphatic linker has been developed. Target molecules were synthesized via a catalytic three-component Ugi reaction from aliphatic diisocyanides. Preliminary investigations proved unspecific nuclease activity of the new compounds towards single-stranded RNA and double-stranded circular DNA.

  18. Topological Optimization of Artificial Microstructure Strategies (United States)


    Topographic Optimization Through Artificial Microstructure Strategies During this project as part of DARPA MCMA we aimed to develop and demonstrate...Topographic Optimization Through Artificial Microstructure Strategies Report Title During this project as part of DARPA MCMA we aimed to develop and...Artificial Microstructure Strategies (Yale and Johns Hopkins) During DARPA MCMA we aimed to develop and demonstrate a 3D microstructural

  19. Artificial Intelligence and Its Importance in Education. (United States)

    Tilmann, Martha J.

    Artificial intelligence, or the study of ideas that enable computers to be intelligent, is discussed in terms of what it is, what it has done, what it can do, and how it may affect the teaching of tomorrow. An extensive overview of artificial intelligence examines its goals and applications and types of artificial intelligence including (1) expert…

  20. Impact of Artificial Intelligence on Economic Theory


    Tshilidzi Marwala


    Artificial intelligence has impacted many aspects of human life. This paper studies the impact of artificial intelligence on economic theory. In particular we study the impact of artificial intelligence on the theory of bounded rationality, efficient market hypothesis and prospect theory.

  1. Motor degradation prediction methods

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, J.R.; Kelly, J.F.; Delzingaro, M.J.


    Motor Operated Valve (MOV) squirrel cage AC motor rotors are susceptible to degradation under certain conditions. Premature failure can result due to high humidity/temperature environments, high running load conditions, extended periods at locked rotor conditions (i.e. > 15 seconds) or exceeding the motor`s duty cycle by frequent starts or multiple valve stroking. Exposure to high heat and moisture due to packing leaks, pressure seal ring leakage or other causes can significantly accelerate the degradation. ComEd and Liberty Technologies have worked together to provide and validate a non-intrusive method using motor power diagnostics to evaluate MOV rotor condition and predict failure. These techniques have provided a quick, low radiation dose method to evaluate inaccessible motors, identify degradation and allow scheduled replacement of motors prior to catastrophic failures.

  2. Solar fuels via artificial photosynthesis. (United States)

    Gust, Devens; Moore, Thomas A; Moore, Ana L


    Because sunlight is diffuse and intermittent, substantial use of solar energy to meet humanity's needs will probably require energy storage in dense, transportable media via chemical bonds. Practical, cost effective technologies for conversion of sunlight directly into useful fuels do not currently exist, and will require new basic science. Photosynthesis provides a blueprint for solar energy storage in fuels. Indeed, all of the fossil-fuel-based energy consumed today derives from sunlight harvested by photosynthetic organisms. Artificial photosynthesis research applies the fundamental scientific principles of the natural process to the design of solar energy conversion systems. These constructs use different materials, and researchers tune them to produce energy efficiently and in forms useful to humans. Fuel production via natural or artificial photosynthesis requires three main components. First, antenna/reaction center complexes absorb sunlight and convert the excitation energy to electrochemical energy (redox equivalents). Then, a water oxidation complex uses this redox potential to catalyze conversion of water to hydrogen ions, electrons stored as reducing equivalents, and oxygen. A second catalytic system uses the reducing equivalents to make fuels such as carbohydrates, lipids, or hydrogen gas. In this Account, we review a few general approaches to artificial photosynthetic fuel production that may be useful for eventually overcoming the energy problem. A variety of research groups have prepared artificial reaction center molecules. These systems contain a chromophore, such as a porphyrin, covalently linked to one or more electron acceptors, such as fullerenes or quinones, and secondary electron donors. Following the excitation of the chromophore, photoinduced electron transfer generates a primary charge-separated state. Electron transfer chains spatially separate the redox equivalents and reduce electronic coupling, slowing recombination of the charge

  3. Photooxidation of cellulose nitrate: new insights into degradation mechanisms. (United States)

    Berthumeyrie, Sebastien; Collin, Steeve; Bussiere, Pierre-Olivier; Therias, Sandrine


    Cellulose nitrate (or nitrocellulose) has received considerable interest due to its uses in various applications, such as paints, photographic films and propellants. However, it is considered as one of the primary pollutants in the energetic material industries because it can be degraded to form polluting chemical species. In this work, the UV light degradation of cellulose nitrate films was studied under conditions of artificially accelerated photooxidation. To eliminate the reactivity of nitro groups, the degradation of ethylcellulose was also investigated. Infrared spectroscopy analyses of the chemical modifications caused by the photooxidation of cellulose nitrate films and the resulting formation of volatile products revealed the occurrence of de-nitration and the formation of oxidation photoproducts exhibiting lactone and anhydride functions. The impact of these chemical modifications on the mechanical and thermal properties of cellulose nitrate films includes embrittlement and lower temperatures of ignition when used as a propellant.

  4. Grassland Degradation and Its Control in Region Around Qinghai Lake

    Institute of Scientific and Technical Information of China (English)



    A quite severe degradation was found in all seven types of grasslands in the study area involiving 12 counties of the northwestern Qinghai Province.The slightly,modeately and severely degraded grasslands occupied 49.7%,32.0%and 18.3% of the area respectively.The major factors resulting in the degradation were overgrazing,the damages from mice and grasshopper and blown sands,and improper use of grasslands,The measures to deal with these probles should be:1) to make livestock development in accordance with grassland carrying capacity for animals;2) to build more artificial grasslands with a stable and higher grass yield;3) to put more widely the rotation grazing system into practice;4) to clear up the poisonous grass species,and 5)to adopt more effective measures to deal with the damages to grasslands by mice and grasshoppers.


    Directory of Open Access Journals (Sweden)

    Julieta Daniela SABĂU (CHELARU


    Full Text Available In recent years, due to increased air pollution, bronze objects exposed in urban areas suffer continuous degradation. Therefore, it is important to find efficient methods to protect them against corrosion. The present work aims to investigate the corrosion resistance of various artificial patina currently used in bronze sculpture. Once formed, the patina is relative stable and acts as a protective coating of the bronze object under many exposure conditions. The protective effect of different artificial patinas was comparatively investigated by electrochemical and non-electrochemical methods.

  6. Antifoam degradation testing

    Energy Technology Data Exchange (ETDEWEB)

    Lambert, D. P. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River Ecology Lab. (SREL); Zamecnik, J. R. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River Ecology Lab. (SREL); Newell, D. D. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River Ecology Lab. (SREL); Williams, M. S. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River Ecology Lab. (SREL)


    This report describes the results of testing to quantify the degradation products resulting from the dilution and storage of Antifoam 747. Antifoam degradation is of concern to the Defense Waste Processing Facility (DWPF) due to flammable decomposition products in the vapor phase of the Chemical Process Cell vessels, as well as the collection of flammable and organic species in the offgas condensate. The discovery that hexamethyldisiloxane is formed from the antifoam decomposition was the basis for a Potential Inadequacy in the Safety Analysis declaration by the DWPF.

  7. Photovoltaic Degradation Risk: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Jordan, D. C.; Kurtz, S. R.


    The ability to accurately predict power delivery over the course of time is of vital importance to the growth of the photovoltaic (PV) industry. Important cost drivers include the efficiency with which sunlight is converted into power, how this relationship changes over time, and the uncertainty in this prediction. An accurate quantification of power decline over time, also known as degradation rate, is essential to all stakeholders - utility companies, integrators, investors, and researchers alike. In this paper we use a statistical approach based on historical data to quantify degradation rates, discern trends and quantify risks related to measurement uncertainties, number of measurements and methodologies.

  8. Glycidol-carbohydrate hybrids: a new family of DNA alkylating agents. (United States)

    Toshima, Kazunobu; Okuno, Yukiko; Matsumura, Shuichi


    Novel and chiral glycidol-carbohydrate hybrids possessing an epoxy group as a DNA alkylating moiety were designed and synthesized. These artificial hybrids selectively alkylated DNA at the N-7 sites of the guanines and cleaved DNA without any additives. The binding ability of the glycidol was significantly enhanced by the attachment of the carbohydrate.

  9. Toxicity of fluorescent tracers and their degradation byproducts

    Directory of Open Access Journals (Sweden)

    Philippe Gombert


    Full Text Available Tracer tests are frequently used to delineate catchment area of water supply springs in karstic zones. In the karstic chalk of Normandy, the main tracers used are fluorescent: uranine, sulforhodamine B, naphtionate, and Tinopal®. In this area, a statistical analysis shows that less than half of the injected tracers joins the monitored restitution points and enters the drinking water system where they undergo chlorination. Most of the injected tracers is absorbed in the rock matrix or is thrown out of the aquifer via karstic springs: then it can join superficial waters where it is degraded due to the sun and air action. The paper presents firstly the laboratory degradation of a first batch of fluorescent tracers in contact with chlorine, in order to simulate their passage through a water treatment system for human consumption. A second batch of the same tracers is subjected to agents of natural degradation: ultraviolet illumination, sunlight and air sparging. Most tracers is degraded, and toxicity and ecotoxicity tests (on rats, daphniae and algae are performed on degradation byproducts. These tests do not show any acute toxicity but a low to moderate ecotoxicity. In conclusion, the most used fluorescent tracers of the Normandy karstic chalk and their artificial and natural degradation byproducts do not exhibit significant toxicity to humans and the aquatic environment, at the concentrations generally noted at the restitution points.

  10. Fragmentation of DNA affects the accuracy of the DNA quantitation by the commonly used methods

    Directory of Open Access Journals (Sweden)

    Sedlackova Tatiana


    Full Text Available Abstract Background Specific applications and modern technologies, like non-invasive prenatal testing, non-invasive cancer diagnostic and next generation sequencing, are currently in the focus of researchers worldwide. These have common characteristics in use of highly fragmented DNA molecules for analysis. Hence, for the performance of molecular methods, DNA concentration is a crucial parameter; we compared the influence of different levels of DNA fragmentation on the accuracy of DNA concentration measurements. Results In our comparison, the performance of the currently most commonly used methods for DNA concentration measurement (spectrophotometric, fluorometric and qPCR based were tested on artificially fragmented DNA samples. In our comparison, unfragmented and three specifically fragmented DNA samples were used. According to our results, the level of fragmentation did not influence the accuracy of spectrophotometric measurements of DNA concentration, while other methods, fluorometric as well as qPCR-based, were significantly influenced and a decrease in measured concentration was observed with more intensive DNA fragmentation. Conclusions Our study has confirmed that the level of fragmentation of DNA has significant impact on accuracy of DNA concentration measurement with two of three mostly used methods (PicoGreen and qPCR. Only spectrophotometric measurement was not influenced by the level of fragmentation, but sensitivity of this method was lowest among the three tested. Therefore if it is possible the DNA quantification should be performed with use of equally fragmented control DNA.

  11. DNA/chitosan electrostatic complex. (United States)

    Bravo-Anaya, Lourdes Mónica; Soltero, J F Armando; Rinaudo, Marguerite


    Up to now, chitosan and DNA have been investigated for gene delivery due to chitosan advantages. It is recognized that chitosan is a biocompatible and biodegradable non-viral vector that does not produce immunological reactions, contrary to viral vectors. Chitosan has also been used and studied for its ability to protect DNA against nuclease degradation and to transfect DNA into several kinds of cells. In this work, high molecular weight DNA is compacted with chitosan. DNA-chitosan complex stoichiometry, net charge, dimensions, conformation and thermal stability are determined and discussed. The influence of external salt and chitosan molecular weight on the stoichiometry is also discussed. The isoelectric point of the complexes was found to be directly related to the protonation degree of chitosan. It is clearly demonstrated that the net charge of DNA-chitosan complex can be expressed in terms of the ratio [NH3(+)]/[P(-)], showing that the electrostatic interactions between DNA and chitosan are the main phenomena taking place in the solution. Compaction of DNA long chain complexed with low molar mass chitosan gives nanoparticles with an average radius around 150nm. Stable nanoparticles are obtained for a partial neutralization of phosphate ionic sites (i.e.: [NH3(+)]/[P(-)] fraction between 0.35 and 0.80).

  12. Tadpole-like artificial micromotor (United States)

    Liu, Limei; Liu, Mei; Su, Yajun; Dong, Yonggang; Zhou, Wei; Zhang, Lina; Zhang, Hui; Dong, Bin; Chi, Lifeng


    We describe a polymer-based artificial tadpole-like micromotor, which is fabricated through the electrospinning technique. By incorporating functional materials onto its surface or within its body, the resulting tadpole-like micromotor can not only move autonomously in an aqueous solution with a flexible tail, but also exhibit thermo- and magnetic responsive properties.We describe a polymer-based artificial tadpole-like micromotor, which is fabricated through the electrospinning technique. By incorporating functional materials onto its surface or within its body, the resulting tadpole-like micromotor can not only move autonomously in an aqueous solution with a flexible tail, but also exhibit thermo- and magnetic responsive properties. Electronic supplementary information (ESI) available: Experimental section, Fig. S1-S3 and Video S1-S4. See DOI: 10.1039/c4nr06621a

  13. Torsional Carbon Nanotube Artificial Muscles (United States)

    Foroughi, Javad; Spinks, Geoffrey M.; Wallace, Gordon G.; Oh, Jiyoung; Kozlov, Mikhail E.; Fang, Shaoli; Mirfakhrai, Tissaphern; Madden, John D. W.; Shin, Min Kyoon; Kim, Seon Jeong; Baughman, Ray H.


    Rotary motors of conventional design can be rather complex and are therefore difficult to miniaturize; previous carbon nanotube artificial muscles provide contraction and bending, but not rotation. We show that an electrolyte-filled twist-spun carbon nanotube yarn, much thinner than a human hair, functions as a torsional artificial muscle in a simple three-electrode electrochemical system, providing a reversible 15,000° rotation and 590 revolutions per minute. A hydrostatic actuation mechanism, as seen in muscular hydrostats in nature, explains the simultaneous occurrence of lengthwise contraction and torsional rotation during the yarn volume increase caused by electrochemical double-layer charge injection. The use of a torsional yarn muscle as a mixer for a fluidic chip is demonstrated.

  14. Penicillium strains as dominant degraders in soil for coffee residue, a biological waste unsuitable for fertilization. (United States)

    Fujii, Katsuhiko; Takeshi, Kyoko


    Coffee residue is an agricultural waste which inhibits the growth of several crops. Therefore coffee residue-degrading microbes in soil were screened, isolated and characterized. Forty isolates were obtained after enrichment culture of soil samples. Seven strains (fast degraders) showed strong degrading activity, while 18 strains (slow degraders) showed weak degrading activity. DNA analysis suggested that the fast degraders are Penicillium, and the slow degraders are Penicillium, Trichoderma/Hypocrea, Fusarium/Gibberella, Phaeoacremonium/Togninia or Acidocella. The all fast degraders are cellulolytic, mannolytic and pectinolytic. Although it is generally thought that fungi such as Trichoderma contribute largely to aerobic degradation of cellulosic biomass, our data suggested that Penicillium overwhelms them in coffee residue degradation. It was implied that polysaccharides in coffee residue are not degraded independently by different microbes, but degraded simultaneously by strains with cellulolytic, mannolytic and pectinolytic activity. Since there is no report of an ascomycete possessing all the three enzyme activities, the fast degraders are ecologically important and have the potential to be used as producers of the costly enzymes from agricultural wastes. The present results advance our understanding of microbial degradation of a phytotoxic agricultural waste, and offer a new tool for recycling it.

  15. Artificial intelligence and computer vision

    CERN Document Server

    Li, Yujie


    This edited book presents essential findings in the research fields of artificial intelligence and computer vision, with a primary focus on new research ideas and results for mathematical problems involved in computer vision systems. The book provides an international forum for researchers to summarize the most recent developments and ideas in the field, with a special emphasis on the technical and observational results obtained in the past few years.

  16. Bioengineering of Artificial Lymphoid Organs


    Nosenko, M. A.; Drutskaya, M. S; M. M. Moisenovich; Nedospasov, S A


    This review addresses the issue of bioengineering of artificial lymphoid organs.Progress in this field may help to better understand the nature of the structure-function relations that exist in immune organs. Artifical lymphoid organs may also be advantageous in the therapy or correction of immunodefficiencies, autoimmune diseases, and cancer. The structural organization, development, and function of lymphoid tissue are analyzed with a focus on the role of intercellular contacts and on the cy...

  17. Artificial color perception using microwaves

    CERN Document Server

    Choudhury, Debesh


    We report the feasibility of artificial color perception under microwave illumination using a standard microwave source and an antenna. We have sensed transmitted microwave power through color objects and have distinguished the colors by analyzing the sensed transmitted power. Experiments are carried out using a Gunn diode as the microwave source, some colored liquids as the objects and a microwave diode as the detector. Results are presented which open up an unusual but new way of perceiving colors using microwaves.

  18. Towards photovoltaic powered artificial retina



    The aim of this article is to provide an overview of current and future concepts in the field of retinal prostheses, and is focused on the power supply based on solar energy conversion; we introduce the possibility of using PV minimodules as power supply for a new concept of retinal prostheses: Photovoltaic Powered Artificial Retina (PVAR). Main characteristics of these PV modules are presented showing its potential for this application. Peer Reviewed

  19. A Definition of Artificial Intelligence



    In this paper we offer a formal definition of Artificial Intelligence and this directly gives us an algorithm for construction of this object. Really, this algorithm is useless due to the combinatory explosion. The main innovation in our definition is that it does not include the knowledge as a part of the intelligence. So according to our definition a newly born baby also is an Intellect. Here we differs with Turing's definition which suggests that an Intellect is a person with knowledge gai...

  20. Artificial color perception using microwaves


    Choudhury, Debesh; Caulfield, H. John


    We report the feasibility of artificial color perception under microwave illumination using a standard microwave source and an antenna. We have sensed transmitted microwave power through color objects and have distinguished the colors by analyzing the sensed transmitted power. Experiments are carried out using a Gunn diode as the microwave source, some colored liquids as the objects and a microwave diode as the detector. Results are presented which open up an unusual but new way of perceiving...