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Sample records for advanced uracil-excision dna

  1. Accurate DNA assembly and genome engineering with optimized uracil excision cloning

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda; Kim, Se Hyeuk; Seppala, Susanna;

    2015-01-01

    produces β-carotene to optimize assembly junctions and the uracil excision protocol. By combining uracil excision cloning with a genomic integration technology, we demonstrate that up to six DNA fragments can be assembled in a one-tube reaction for direct genome integration with high accuracy, greatly...

  2. Perturbations of enzymic uracil excision due to purine damage in DNA.

    OpenAIRE

    Duker, N J; Jensen, D E; Hart, D M; Fishbein, D E

    1982-01-01

    Phage PBS-2 DNA, which contains uracil in place of thymine, was selectively damaged and then used as substrate for purified Bacillus subtilis uracil-DNA glycosylase. This enzyme releases uracil from DNA in a limited processive manner. Irradiation by ultraviolet light (greater than 305 nm) in the presence of isopropanol and a free radical photoinitiator introduced covalently bound 8-(2-hydroxy-2-propyl)purines into DNA. Methylation by dimethylsulfate yielded 7-methylguanine. Apurinic sites wer...

  3. Accurate Dna Assembly And Direct Genome Integration With Optimized Uracil Excision Cloning To Facilitate Engineering Of Escherichia Coli As A Cell Factory

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda; Kim, Se Hyeuk; Nørholm, Morten

    2015-01-01

    Plants produce a vast diversity of valuable compounds with medical properties, but these are often difficult to purify from the natural source or produce by organic synthesis. An alternative is to transfer the biosynthetic pathways to an efficient production host like the bacterium Escherichia co......-excision-based cloning and combining it with a genome-engineering approach to allow direct integration of whole metabolic pathways into the genome of E. coli, to facilitate the advanced engineering of cell factories....

  4. G-quadruplex DNA structures can interfere with uracil glycosylase activity in vitro.

    Science.gov (United States)

    Holton, Nate W; Larson, Erik D

    2016-07-01

    Genome sequences that contain tandem repeats of guanine can form stable four-stranded structures known as G-quadruplex, or G4 DNA. While the molecular mechanisms are not fully defined, such guanine-rich loci are prone to mutagenesis and recombination. Various repair pathways function to reduce the potential for genome instability by correcting base damage and replication errors; however, it is not yet fully defined how well these processes function at G4 DNA. One frequent form of base damage occurs from cytidine deamination, resulting in deoxyuracil and UG mismatches. In duplex and single-stranded DNA, uracil bases are recognised and excised by uracil glycosylases. Here, we tested the efficiency of uracil glycosylase activity in vitro on uracil bases located directly adjacent to guanine repeats and G4 DNA. We show that uracil excision by bacterial UDG and human hUNG2 is reduced at uracils positioned directly 5' or 3' of a guanine tetrad. Control reactions using oligonucleotides disrupted for G4 formation or reaction conditions that do not favour G4 formation resulted in full uracil excision activity. Based on these in vitro results, we suggest that folding of guanine-rich DNA into G4 DNA results in a DNA conformation that is resistant to uracil glycosylase-initiated repair and this has the potential to increase the risk of instability at guanine repeats in the genome. PMID:26671821

  5. Review on the Advancements of DNA Cryptography

    CERN Document Server

    Anam, Beenish; Hossain, Md Alamgir; Dahal, Keshav

    2010-01-01

    Since security is one of the most important issues, the evolve of cryptography and cryptographic analysis are considered as the fields of on-going research. The latest development on this field is DNA cryptography. It has emerged after the disclosure of computational ability of Deoxyribo Nucleic Acid (DNA). DNA cryptography uses DNA as the computational tool along with several molecular techniques to manipulate it. Due to very high storage capacity of DNA, this field is becoming very promising. Currently it is in the development phase and it requires a lot of work and research to reach a mature stage. By reviewing all the potential and cutting edge technology of current research, this paper shows the directions that need to be addressed further in the field of DNA cryptography.

  6. Advancing taxonomy and bioinventories with DNA barcodes.

    Science.gov (United States)

    Miller, Scott E; Hausmann, Axel; Hallwachs, Winnie; Janzen, Daniel H

    2016-09-01

    We use three examples-field and ecology-based inventories in Costa Rica and Papua New Guinea and a museum and taxonomic-based inventory of the moth family Geometridae-to demonstrate the use of DNA barcoding (a short sequence of the mitochondrial COI gene) in biodiversity inventories, from facilitating workflows of identification of freshly collected specimens from the field, to describing the overall diversity of megadiverse taxa from museum collections, and most importantly linking the fresh specimens, the general museum collections and historic type specimens. The process also flushes out unexpected sibling species hiding under long-applied scientific names, thereby clarifying and parsing previously mixed collateral data. The Barcode of Life Database has matured to an essential interactive platform for the multi-authored and multi-process collaboration. The BIN system of creating and tracking DNA sequence-based clusters as proxies for species has become a powerful way around some parts of the 'taxonomic impediment', especially in entomology, by providing fast but testable and tractable species hypotheses, tools for visualizing the distribution of those in time and space and an interim naming system for communication.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481791

  7. Recent advances in DNA sequencing techniques

    Science.gov (United States)

    Singh, Rama Shankar

    2013-06-01

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

  8. DNA Vaccines against Protozoan Parasites: Advances and Challenges

    Directory of Open Access Journals (Sweden)

    Eric Dumonteil

    2007-01-01

    Full Text Available Over the past 15 years, DNA vaccines have gone from a scientific curiosity to one of the most dynamic research field and may offer new alternatives for the control of parasitic diseases such as leishmaniasis and Chagas disease. We review here some of the advances and challenges for the development of DNA vaccines against these diseases. Many studies have validated the concept of using DNA vaccines for both protection and therapy against these protozoan parasites in a variety of mouse models. The challenge now is to translate what has been achieved in these models into veterinary or human vaccines of comparable efficacy. Also, genome-mining and new antigen discovery strategies may provide new tools for a more rational search of novel vaccine candidates.

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

    Science.gov (United States)

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

    2015-12-01

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

  10. Use of sequence microdivergence in mycobacterial ortholog to analyze contributions of the water-activating loop histidine of Escherichia coli uracil-DNA glycosylase in reactant binding and catalysis

    International Nuclear Information System (INIS)

    Uracil-DNA glycosylase (Ung), a DNA repair enzyme, pioneers uracil excision repair pathway. Structural determinations and mutational analyses of the Ung class of proteins have greatly facilitated our understanding of the mechanism of uracil excision from DNA. More recently, a hybrid quantum-mechanical/molecular mechanical analysis revealed that while the histidine (H67 in EcoUng) of the GQDPYH motif (ω loop) in the active site pocket is important in positioning the reactants, it makes an unfavorable energetic contribution (penalty) in achieving the transition state intermediate. Mutational analysis of this histidine is unavailable from any of the Ung class of proteins. A complication in demonstrating negative role of a residue, especially when located within the active site pocket, is that the mutants with enhanced activity are rarely obtained. Interestingly, unlike the most Ung proteins, the H67 equivalent in the ω loop in mycobacterial Ung is represented by P67. Exploiting this natural diversity to maintain structural integrity of the active site, we transplanted an H67P mutation in EcoUng. Uracil inhibition assays and binding of a proteinaceous inhibitor, Ugi (a transition state substrate mimic), with the mutant (H67P) revealed that its active site pocket was not perturbed. The catalytic efficiency (Vmax/Km) of the mutant was similar to that of the wild type Ung. However, the mutant showed increased Km and Vmax. Together with the data from a double mutation H67P/G68T, these observations provide the first biochemical evidence for the proposed diverse roles of H67 in catalysis by Ung

  11. Recent advances in DNA technology for communicable diseases

    International Nuclear Information System (INIS)

    Advances in DNA technology have benefitted every area of biological research in the past several years. A wide variety of new techniques are being developed that will enable researchers to address old and unsolved problems. The polymerase-catalyzed chain reaction (PCR) and the exponential replication of recombinant-RNA hybridization probes using the RNA Replicase of the bacteriophage QΒ are two of these techniques. Both methods offer powerful means of amplifying specific nucleic acid sequences and can render it possible to perform tasks which will be very useful in studies related to communicable diseases. Among such applications is the development of extremely sensitive molecular reagents for diagnosis of infectious agents. (author). 10 refs

  12. Advances in Research on Hepatitis B Virus DNA Integration

    Institute of Scientific and Technical Information of China (English)

    Ju-sheng LIN; Lin-lin GAO

    2008-01-01

    Since HBV DNA integration was discovered for the first time in 1980, various methods have been used to detect and study it, such as Southern Blot, in situ hybridization, polymerase chain reaction and so on. HBV DNA integration is thought to be random on the whole although some hot spots of integration were described by some researchers, one of which might be the repetitive sequences of the genomic DNA. Besides, DNA damage, especially double-strand breaks could promote HBV DNA integration into host genome. HBV DNA integration into cells may damage the stability of the genome, cause DNA rearrangement, promote DNA deletion and induce the formation of HCC.

  13. Structure of uracil-DNA glycosylase from Mycobacterium tuberculosis: insights into interactions with ligands

    International Nuclear Information System (INIS)

    The molecule of uracil-DNA glycosylase from M. tuberculosis exhibits domain motion on binding to DNA or a proteinaceous inhibitor. The highly conserved DNA-binding region interacts with a citrate ion in the structure. Uracil N-glycosylase (Ung) is the most thoroughly studied of the group of uracil DNA-glycosylase (UDG) enzymes that catalyse the first step in the uracil excision-repair pathway. The overall structure of the enzyme from Mycobacterium tuberculosis is essentially the same as that of the enzyme from other sources. However, differences exist in the N- and C-terminal stretches and some catalytic loops. Comparison with appropriate structures indicate that the two-domain enzyme closes slightly when binding to DNA, while it opens slightly when binding to the proteinaceous inhibitor Ugi. The structural changes in the catalytic loops on complexation reflect the special features of their structure in the mycobacterial protein. A comparative analysis of available sequences of the enzyme from different sources indicates high conservation of amino-acid residues in the catalytic loops. The uracil-binding pocket in the structure is occupied by a citrate ion. The interactions of the citrate ion with the protein mimic those of uracil, in addition to providing insights into other possible interactions that inhibitors could be involved in

  14. Recent advances in yeast molecular biology: recombinant DNA. [Lead abstract

    Energy Technology Data Exchange (ETDEWEB)

    1982-09-01

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis. (KRM)

  15. Recent advances in yeast molecular biology: recombinant DNA

    International Nuclear Information System (INIS)

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis

  16. Advances Achieved on Studies of East Asian mtDNA Phylogeny

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ Agroup of geneticists at the CAS Kunming Institute of Zoology (KIZ)succeeded in advancing out knowledge on the East Asian phylogeny of human mitochondrial DNA (mtDNA). Their work, which was finished by Dr. Kong Qingpeng under the guidance of ZHANG Yaping, was published by the journal Human Molecular Genetics.

  17. What Advances Are Being Made in DNA Sequencing?

    Science.gov (United States)

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

  18. Research Advances in Pituitary Adenoma and DNA Methylation.

    Science.gov (United States)

    Wei, Zhen-Qing; Li, Yang; Li, Wei-Hua; Lou, Jia-Cheng; Zhang, Bo

    2016-08-01

    DNA methylation is closely related to the genesis and development of pituitary adenoma. Studies have shown that high methylation in the promoter region of potassium voltage-gated chanel,shaker related subfamily,beta member 2,O-6-methylguanine-DNA methyltransferase,echinoderm microtubule associated protein like 2 ,ras homolog family member D ,homeobox B1 ,NNAT, and P16 inhibits the expression of these genes and regulates of the proliferation of pituitary adenoma. DNA methylation is also closely related to invasive pituitary adenoma. Therefore,further study on molecular mechanism of DNA methylation of pituitary adenoma will offer a new strategy for the diagnosis and treatment of pituitary adenoma. PMID:27594164

  19. 酶促DNA合成研究的进展%Advance in Enzymatic DNA Synthesis

    Institute of Scientific and Technical Information of China (English)

    向义和

    2011-01-01

    The advance in enzymatic DNA synthesis is introduced. Kornberg and his colleagues went through deoxyribonucleotide.de-oxynucleoside try phosphates and DNA synthesis. The immediate precursor of DNA synthesis was known. DNA polymerase was separated and purified. The chemical mechanism of DNA synthesis was revealed and infectious phage φX174DNA was synthesized.%笔者介绍了酶促DNA合成研究的进展.科恩伯格和他的同事经历了从合成核苷酸、核苷三磷酸到合成DNA的历程.他们分离并提纯了DNA聚合酶,弄清了合成DNA的最直接的前体,揭示了DNA合成的化学机理,合成了具有感染性的噬菌体φX174DNA.

  20. Advancing DNA-based Nanotechnology Capabilities and Applications

    Science.gov (United States)

    Marchi, Alexandria N.

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

  1. Levels of cell-free DNA and plasma KRAS during treatment of advanced NSCLC

    DEFF Research Database (Denmark)

    Dowler Nygaard, Anneli; Spindler, Karen-Lise Garm; Pallisgaard, Niels;

    2014-01-01

    Non-small cell lung cancer (NSCLC) is one of the most common malignant tumours in the western world and is associated with a poor prognosis. Biomarkers predicting prognosis and therapeutic effects are highly required, and cell-free DNA (cfDNA) may be a feasible option. Genetic mutations can be...... analysed in plasma and may increase the scientific use of such measurements. In the present study, we investigated: i) the dynamics of cfDNA and plasma mutated KRAS (pmKRAS) during the treatment of patients with advanced NSCLC; and ii) the prognostic value of baseline cfDNA and pmKRAS. Sixty‑nine patients...... were included in a prospective biomarker trial. Inclusion criteria included advanced NSCLC, candidate for first-line treatment, no previous cancer within the five years prior to this study. Blood samples were drawn at baseline, day 8 and at progression. Analyses of cfDNA and KRAS mutations in plasma...

  2. Advances on circulating fetal DNA in maternal plasma

    Institute of Scientific and Technical Information of China (English)

    FU Xian-hu; CHEN Han-ping

    2007-01-01

    @@ The discovery of cell-free fetal DNA in maternal plasma in 1997 has opened up new possibilities for noninvasive diagnosis.1 By RT-PCR, circulating fetal DNA can be detected in the plasma of pregnant women,even in the first trimester of pregnancy,2,3 and thus can be used for noninvasive prenatal diagnosis of sex-linked disorders,4-6 the RhD status of fetuses,7 and single gene disorders such as beta-thalassaemia,8,9 congenital adrenal hyperplasia,10 and achondroplasia.11 In addition,quantitative aberrations of circulating fetal DNA may indicate various pregnancy-associated disorders,including1 Preeclampsia,12-14 preterm labor15,16 and fetal trisomy 21.17

  3. Blocking DNA Repair in Advanced BRCA-Mutated Cancer

    Science.gov (United States)

    In this trial, patients with relapsed or refractory advanced cancer and confirmed BRCA mutations who have not previously been treated with a PARP inhibitor will be given BMN 673 by mouth once a day in 28-day cycles.

  4. DNA methylation in cardiac fibrosis: New advances and perspectives

    International Nuclear Information System (INIS)

    Cardiac fibrosis is characterized by net accumulation of extracellular matrix (ECM) proteins in the cardiac interstitium, and contributes to both systolic and diastolic dysfunction in many cardiac pathophysiologic conditions. More specifically, cardiac fibroblasts are activated by a variety of pathological stimuli, thereby undergoing proliferation, differentiation to myofibroblasts, and production of various cytokines and ECM proteins. Thus, understanding the biological processes of cardiac fibroblasts will provide novel insights into the underlying mechanisms of cardiac fibrosis. DNA methylation is an important epigenetic mechanism, which often occurs in response to environmental stimuli and is crucial in regulating gene expression. The aberrant methylation of CpG island promoters of selected genes is the prominent epigenetic mechanism by which gene transcription can be effectively silenced. Aberrant hypermethylation of a few selected genes such as RASSF1A plays an important role in facilitating fibrotic fibroblast activation and in driving fibrosis. In this review we will discuss the mechanisms of DNA methylation and their implications for cardiac fibroblasts activation and fibrosis. Control of DNA methylation may serve as a new strategy for anti-fibrotic therapy

  5. Advances in DNA metabarcoding for food and wildlife forensic species identification.

    Science.gov (United States)

    Staats, Martijn; Arulandhu, Alfred J; Gravendeel, Barbara; Holst-Jensen, Arne; Scholtens, Ingrid; Peelen, Tamara; Prins, Theo W; Kok, Esther

    2016-07-01

    Species identification using DNA barcodes has been widely adopted by forensic scientists as an effective molecular tool for tracking adulterations in food and for analysing samples from alleged wildlife crime incidents. DNA barcoding is an approach that involves sequencing of short DNA sequences from standardized regions and comparison to a reference database as a molecular diagnostic tool in species identification. In recent years, remarkable progress has been made towards developing DNA metabarcoding strategies, which involves next-generation sequencing of DNA barcodes for the simultaneous detection of multiple species in complex samples. Metabarcoding strategies can be used in processed materials containing highly degraded DNA e.g. for the identification of endangered and hazardous species in traditional medicine. This review aims to provide insight into advances of plant and animal DNA barcoding and highlights current practices and recent developments for DNA metabarcoding of food and wildlife forensic samples from a practical point of view. Special emphasis is placed on new developments for identifying species listed in the Convention on International Trade of Endangered Species (CITES) appendices for which reliable methods for species identification may signal and/or prevent illegal trade. Current technological developments and challenges of DNA metabarcoding for forensic scientists will be assessed in the light of stakeholders' needs. PMID:27178552

  6. Multiple origins of advanced eusociality in bees inferred from mitochondrial DNA sequences.

    OpenAIRE

    Cameron, S. A.

    1993-01-01

    The remarkably high level of colony organization found in the honey bees and stingless bees (family Apidae) is extremely rare among animals. Yet there is controversy over whether these two groups independently evolved advanced eusocial behavior or inherited it from a common ancestor. Phylogenetic analyses of DNA sequence information from the mitochondrial genome (large-subunit ribosomal RNA gene) of representative apid bees suggest that advanced eusocial behavior evolved twice independently w...

  7. Rust resistance evaluation of advanced wheat (triticum aestivum l.) genotypes using pcr-based dna markers

    International Nuclear Information System (INIS)

    The most effective and environmental friendly approach for the control of wheat rust disease is the use of resistant genotypes. The present study was conducted to explore rust resistance potential of 85 elite wheat genotypes (36 varieties and 49 advanced lines) using various types of DNA markers like STS, SCAR and SSR. DNA markers linked with different genes conferring resistance to rusts (Leaf rust=Lr, Yellow rust=Yr and Stem rust=Sr) were employed in this study. A total of 18 genes, consisting of eleven Lr (lr1, lr10, lr19, lr21, lr28, lr34, lr39, lr46, lr47, lr51 and lr52), four Yr (yr5, yr18, yr26 and yr29) and three Sr genes (sr2, sr29, and sr36) were studied through linked DNA markers. Maximum number of Lr genes was found in 17 advanced lines and 9 varieties, Yr genes in 26 advanced lines and 20 wheat varieties, and Sr genes in 43 advanced lines and 27 varieties. Minimum number of Lr genes was found in advanced line D-97 and variety Kohinoor-83, Yr genes in wheat variety Bwp-97 and Sr genes in 6 advanced lines and 8 varieties. Molecular data revealed that genotypes having same origin, from a specified area showed resistance for similar type of genes. In this study, an average similarity of 84% was recorded among wheat genotypes. Out of 18 loci, 15 were found to be polymorphic. (author)

  8. Advances in radiation biology: Radiosensitization in DNA and living cells

    Science.gov (United States)

    Lacombe, S.; Sech, C. Le

    2009-06-01

    One fundamental goal of radiation biology is the evolution of concepts and methods for the elaboration of new approaches and protocols for the treatment of cancers. In this context, the use of fast ions as ionizing particles offers the advantage of optimizing cell killing inside the tumor whilst preserving the surrounding healthy tissues. One extremely promising strategy investigated recently is the addition of radiosensitizers in the targeted tissue. The optimization of radiotherapy with fast ions implies a multidisciplinary approach to ionizing radiation effects on complex living systems, ranging from studies on single molecules to investigations of entire organisms. In this article we review recent studies on ion induced damages in simple and complex biological systems, from DNA to living cells. The specific aspect of radiosensitization induced by metallic atoms is described. As a fundamental result, the addition of sensitizing compounds with ion irradiation may improve therapeutic index in cancer therapy. In conclusion, new perspectives are proposed based on the experience and contribution of different communities including Surface Sciences, to improve the development of radiation biology.

  9. Assessing macroinvertebrate biodiversity in freshwater ecosystems: Advances and challenges in dna-based approaches

    Science.gov (United States)

    Pfrender, M.E.; Ferrington, L.C., Jr.; Hawkins, C.P.; Hartzell, P.L.; Bagley, M.; Jackson, S.; Courtney, G.W.; Larsen, D.P.; Creutzburg, B.R.; Levesque, C.A.; Epler, J.H.; Morse, J.C.; Fend, S.; Petersen, M.J.; Ruiter, D.; Schindel, D.; Whiting, M.

    2010-01-01

    Assessing the biodiversity of macroinvertebrate fauna in freshwater ecosystems is an essential component of both basic ecological inquiry and applied ecological assessments. Aspects of taxonomic diversity and composition in freshwater communities are widely used to quantify water quality and measure the efficacy of remediation and restoration efforts. The accuracy and precision of biodiversity assessments based on standard morphological identifications are often limited by taxonomic resolution and sample size. Morphologically based identifications are laborious and costly, significantly constraining the sample sizes that can be processed. We suggest that the development of an assay platform based on DNA signatures will increase the precision and ease of quantifying biodiversity in freshwater ecosystems. Advances in this area will be particularly relevant for benthic and planktonic invertebrates, which are often monitored by regulatory agencies. Adopting a genetic assessment platform will alleviate some of the current limitations to biodiversity assessment strategies. We discuss the benefits and challenges associated with DNA-based assessments and the methods that are currently available. As recent advances in microarray and next-generation sequencing technologies will facilitate a transition to DNA-based assessment approaches, future research efforts should focus on methods for data collection, assay platform development, establishing linkages between DNA signatures and well-resolved taxonomies, and bioinformatics. ?? 2010 by The University of Chicago Press.

  10. Radiation induced apoptosis and initial DNA damage are inversely related in locally advanced breast cancer patients

    Directory of Open Access Journals (Sweden)

    Rodriguez-Gallego Carlos

    2010-09-01

    Full Text Available Abstract Background DNA-damage assays, quantifying the initial number of DNA double-strand breaks induced by radiation, have been proposed as a predictive test for radiation-induced toxicity. Determination of radiation-induced apoptosis in peripheral blood lymphocytes by flow cytometry analysis has also been proposed as an approach for predicting normal tissue responses following radiotherapy. The aim of the present study was to explore the association between initial DNA damage, estimated by the number of double-strand breaks induced by a given radiation dose, and the radio-induced apoptosis rates observed. Methods Peripheral blood lymphocytes were taken from 26 consecutive patients with locally advanced breast carcinoma. Radiosensitivity of lymphocytes was quantified as the initial number of DNA double-strand breaks induced per Gy and per DNA unit (200 Mbp. Radio-induced apoptosis at 1, 2 and 8 Gy was measured by flow cytometry using annexin V/propidium iodide. Results Radiation-induced apoptosis increased in order to radiation dose and data fitted to a semi logarithmic mathematical model. A positive correlation was found among radio-induced apoptosis values at different radiation doses: 1, 2 and 8 Gy (p Conclusions An inverse association was observed for the first time between these variables, both considered as predictive factors to radiation toxicity.

  11. Radiation induced apoptosis and initial DNA damage are inversely related in locally advanced breast cancer patients

    International Nuclear Information System (INIS)

    DNA-damage assays, quantifying the initial number of DNA double-strand breaks induced by radiation, have been proposed as a predictive test for radiation-induced toxicity. Determination of radiation-induced apoptosis in peripheral blood lymphocytes by flow cytometry analysis has also been proposed as an approach for predicting normal tissue responses following radiotherapy. The aim of the present study was to explore the association between initial DNA damage, estimated by the number of double-strand breaks induced by a given radiation dose, and the radio-induced apoptosis rates observed. Peripheral blood lymphocytes were taken from 26 consecutive patients with locally advanced breast carcinoma. Radiosensitivity of lymphocytes was quantified as the initial number of DNA double-strand breaks induced per Gy and per DNA unit (200 Mbp). Radio-induced apoptosis at 1, 2 and 8 Gy was measured by flow cytometry using annexin V/propidium iodide. Radiation-induced apoptosis increased in order to radiation dose and data fitted to a semi logarithmic mathematical model. A positive correlation was found among radio-induced apoptosis values at different radiation doses: 1, 2 and 8 Gy (p < 0.0001 in all cases). Mean DSB/Gy/DNA unit obtained was 1.70 ± 0.83 (range 0.63-4.08; median, 1.46). A statistically significant inverse correlation was found between initial damage to DNA and radio-induced apoptosis at 1 Gy (p = 0.034). A trend toward 2 Gy (p = 0.057) and 8 Gy (p = 0.067) was observed after 24 hours of incubation. An inverse association was observed for the first time between these variables, both considered as predictive factors to radiation toxicity

  12. The Extraction and Partial Purification of Bacterial DNA as a Practical Exercise for GCE Advanced Level Students.

    Science.gov (United States)

    Falconer, A. C.; Hayes, L. J.

    1986-01-01

    Describes a relatively simple method of extraction and purification of bacterial DNA. This technique permits advanced secondary-level science students to obtain adequate amounts of DNA from very small pellets of bacteria and to observe some of its polymer properties. (ML)

  13. Variable copy number of mitochondrial DNA (mtDNA) predicts worse prognosis in advanced gastric cancer patients

    OpenAIRE

    Zhang, Guanjun; Qu, Yiping; Dang, Siwen; Yang, Qi; Shi, Bingyin; Hou, Peng

    2013-01-01

    Background Change of mitochondrial DNA (mtDNA) copy number is widely reported in various human cancers, including gastric cancer, and is considered to be an important hallmark of cancers. However, there is remarkably little consensus on the value of variable mtDNA content in the prognostic evaluation of this cancer. Methods Using real-time quantitative PCR approach, we examined mtDNA copy number in a cohort of gastric cancers and normal gastric tissues, and explored the association of variabl...

  14. Circulating tumor DNA identified by targeted sequencing in advanced-stage non-small cell lung cancer patients.

    Science.gov (United States)

    Xu, Song; Lou, Feng; Wu, Yi; Sun, Da-Qiang; Zhang, Jing-Bo; Chen, Wei; Ye, Hua; Liu, Jing-Hao; Wei, Sen; Zhao, Ming-Yu; Wu, Wen-Jun; Su, Xue-Xia; Shi, Rong; Jones, Lindsey; Huang, Xue F; Chen, Si-Yi; Chen, Jun

    2016-01-28

    Non-small cell lung cancers (NSCLC) have unique mutation patterns, and some of these mutations may be used to predict prognosis or guide patient treatment. Mutation profiling before and during treatment often requires repeated tumor biopsies, which is not always possible. Recently, cell-free, circulating tumor DNA (ctDNA) isolated from blood plasma has been shown to contain genetic mutations representative of those found in the primary tumor tissue DNA (tDNA), and these samples can readily be obtained using non-invasive techniques. However, there are still no standardized methods to identify mutations in ctDNA. In the current study, we used a targeted sequencing approach with a semi-conductor based next-generation sequencing (NGS) platform to identify gene mutations in matched tDNA and ctDNA samples from 42 advanced-stage NSCLC patients from China. We identified driver mutations in matched tDNA and ctDNA in EGFR, KRAS, PIK3CA, and TP53, with an overall concordance of 76%. In conclusion, targeted sequencing of plasma ctDNA may be a feasible option for clinical monitoring of NSCLC in the near future. PMID:26582655

  15. Impact of Plasma Epstein-Barr Virus-DNA and Tumor Volume on Prognosis of Locally Advanced Nasopharyngeal Carcinoma

    Directory of Open Access Journals (Sweden)

    Meng Chen

    2015-01-01

    Full Text Available This retrospective study aims to examine the association of plasma Epstein-Barr virus- (EBV- DNA levels with the tumor volume and prognosis in patients with locally advanced nasopharyngeal carcinoma (NPC. A total of 165 patients with newly diagnosed locally advanced NPC were identified from September 2011 to July 2012. EBV-DNA was detected using fluorescence quantitative polymerase chain reaction (PCR amplification. The tumor volume was calculated by the systematic summation method of computer software. The median copy number of plasma EBV-DNA before treatment was 3790 copies/mL. The median gross tumor volume of the primary nasopharyngeal tumor (GTVnx, the lymph node lesions (GTVnd, and the total GTV before treatment were 72.46, 23.26, and 106.25 cm3, respectively; the EBV-DNA levels were significantly correlated with the GTVnd and the total GTV (P<0.01. The 2-year overall survival (OS rates in patients with positive and negative pretreatment plasma EBV-DNA were 100% and 98.4% (P=1.000, and the disease-free survival (DFS rates were 94.4% and 80.8% (P=0.044, respectively. These results indicate that high pretreatment plasma EBV-DNA levels in patients with locally advanced NPC are associated with the degree of lymph node metastasis, tumor burden, and poor prognosis.

  16. The prognostic value of KRAS mutated plasma DNA in advanced non-small cell lung cancer

    DEFF Research Database (Denmark)

    Nygaard, Anneli Dowler; Garm Spindler, Karen-Lise; Pallisgaard, Niels;

    2013-01-01

    BACKGROUND: Lung cancer is one of the most common malignant diseases worldwide and associated with considerable morbidity and mortality. New agents targeting the epidermal growth factor system are emerging, but only a subgroup of the patients will benefit from the therapy. Cell free DNA (cf......DNA) in the blood allows for tumour specific analyses, including KRAS-mutations, and the aim of the study was to investigate the possible prognostic value of plasma mutated KRAS (pmKRAS) in patients with non-small cell lung cancer (NSCLC). MATERIAL AND METHODS: Patients with newly diagnosed, advanced NSCLC eligible......-KRAS mutation had a significantly shorter OS and PFS compared to the wild type (WT) patients (median OS 4.8 months versus 9.5 months, HR 1.87, 95% CI 1.23-2.84, p=0.0002 and median PFS 3.0 months versus 5.6 months, HR 1.60, 95% CI 1.09-2.37, p=0.0043). A multivariate Cox regression analysis confirmed...

  17. Actionable mutations in plasma cell-free DNA in patients with advanced cancers referred for experimental targeted therapies

    OpenAIRE

    Janku, Filip; Angenendt, Philipp; Tsimberidou, Apostolia M.; Fu, Siqing; Naing, Aung; Falchook, Gerald S.; David S Hong; Holley, Veronica R.; Cabrilo, Goran; Jennifer J Wheler; Piha-Paul, Sarina A.; Zinner, Ralph G.; Bedikian, Agop Y.; Overman, Michael J.; Kee, Bryan K.

    2015-01-01

    Cell-free (cf) DNA in the plasma of cancer patients offers an easily obtainable source of biologic material for mutation analysis. Plasma samples from 157 patients with advanced cancers who progressed on systemic therapy were tested for 21 mutations in BRAF, EGFR, KRAS, and PIK3CA using the BEAMing method and results were compared to mutation analysis of archival tumor tissue from a CLIA-certified laboratory obtained as standard of care from diagnostic or therapeutic procedures. Results were ...

  18. Actionable mutations in plasma cell-free DNA in patients with advanced cancers referred for experimental targeted therapies

    Science.gov (United States)

    Janku, Filip; Angenendt, Philipp; Tsimberidou, Apostolia M.; Fu, Siqing; Naing, Aung; Falchook, Gerald S.; Hong, David S.; Holley, Veronica R.; Cabrilo, Goran; Wheler, Jennifer J.; Piha-Paul, Sarina A.; Zinner, Ralph G.; Bedikian, Agop Y.; Overman, Michael J.; Kee, Bryan K.; Kim, Kevin B.; Kopetz, E. Scott; Luthra, Rajyalakshmi; Diehl, Frank; Meric-Bernstam, Funda; Kurzrock, Razelle

    2015-01-01

    Cell-free (cf) DNA in the plasma of cancer patients offers an easily obtainable source of biologic material for mutation analysis. Plasma samples from 157 patients with advanced cancers who progressed on systemic therapy were tested for 21 mutations in BRAF, EGFR, KRAS, and PIK3CA using the BEAMing method and results were compared to mutation analysis of archival tumor tissue from a CLIA-certified laboratory obtained as standard of care from diagnostic or therapeutic procedures. Results were concordant for archival tissue and plasma cfDNA in 91% cases for BRAF mutations (kappa = 0.75, 95% confidence interval [CI] 0.63 – 0.88), in 99% cases for EGFR mutations (kappa = 0.90, 95% CI 0.71– 1.00), in 83% cases for KRAS mutations (kappa = 0.67, 95% CI 0.54 – 0.80) and in 91% cases for PIK3CA mutations (kappa = 0.65, 95% CI 0.46 – 0.85). Patients (n = 41) with > 1% of KRAS mutant cfDNA had a shorter median survival compared to 20 patients with 1% of mutant cfDNA (BRAF, EGFR, KRAS, or PIK3CA) had a shorter median survival compared to 33 patients with DNA (5.5 vs. 9.8 months, p = 0.001), which was confirmed in multivariable analysis. PMID:25980577

  19. DNA and RNA sensor

    Institute of Scientific and Technical Information of China (English)

    LIU; Tao; LIN; Lin; ZHAO; Hong; JIANG; Long

    2005-01-01

    This review summarizes recent advances in DNA sensor. Major areas of DNA sensor covered in this review include immobilization methods of DNA, general techniques of DNA detection and application of nanoparticles in DNA sensor.

  20. DNA cleavage enzymes for treatment of persistent viral infections: Recent advances and the pathway forward

    International Nuclear Information System (INIS)

    Treatment for most persistent viral infections consists of palliative drug options rather than curative approaches. This is often because long-lasting viral DNA in infected cells is not affected by current antivirals, providing a source for viral persistence and reactivation. Targeting latent viral DNA itself could therefore provide a basis for novel curative strategies. DNA cleavage enzymes can be used to induce targeted mutagenesis of specific genes, including those of exogenous viruses. Although initial in vitro and even in vivo studies have been carried out using DNA cleavage enzymes targeting various viruses, many questions still remain concerning the feasibility of these strategies as they transition into preclinical research. Here, we review the most recent findings on DNA cleavage enzymes for human viral infections, consider the most relevant animal models for several human viral infections, and address issues regarding safety and enzyme delivery. Results from well-designed in vivo studies will ideally provide answers to the most urgent remaining questions, and allow continued progress toward clinical application. - Highlights: • Recent in vitro and in vivo results for DNA cleavage enzymes targeting persistent viral infections. • Analysis of the best animal models for testing enzymes for HBV, HSV, HIV and HPV. • Challenges facing in vivo delivery of therapeutic enzymes for persistent viral infections. • Safety issues to be addressed with proper animal studies

  1. DNA cleavage enzymes for treatment of persistent viral infections: Recent advances and the pathway forward

    Energy Technology Data Exchange (ETDEWEB)

    Weber, Nicholas D., E-mail: nweber@fhcrc.org [Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, E5-110, Seattle, WA 98109 (United States); Department of Laboratory Medicine, University of Washington, Seattle, WA 98195 (United States); Aubert, Martine, E-mail: maubert@fhcrc.org [Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, E5-110, Seattle, WA 98109 (United States); Dang, Chung H., E-mail: cdang@fhcrc.org [Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, E5-110, Seattle, WA 98109 (United States); Stone, Daniel, E-mail: dstone2@fhcrc.org [Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, E5-110, Seattle, WA 98109 (United States); Jerome, Keith R., E-mail: kjerome@fhcrc.org [Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, E5-110, Seattle, WA 98109 (United States); Department of Laboratory Medicine, University of Washington, Seattle, WA 98195 (United States); Department of Microbiology, University of Washington, Seattle, WA 98195 (United States)

    2014-04-15

    Treatment for most persistent viral infections consists of palliative drug options rather than curative approaches. This is often because long-lasting viral DNA in infected cells is not affected by current antivirals, providing a source for viral persistence and reactivation. Targeting latent viral DNA itself could therefore provide a basis for novel curative strategies. DNA cleavage enzymes can be used to induce targeted mutagenesis of specific genes, including those of exogenous viruses. Although initial in vitro and even in vivo studies have been carried out using DNA cleavage enzymes targeting various viruses, many questions still remain concerning the feasibility of these strategies as they transition into preclinical research. Here, we review the most recent findings on DNA cleavage enzymes for human viral infections, consider the most relevant animal models for several human viral infections, and address issues regarding safety and enzyme delivery. Results from well-designed in vivo studies will ideally provide answers to the most urgent remaining questions, and allow continued progress toward clinical application. - Highlights: • Recent in vitro and in vivo results for DNA cleavage enzymes targeting persistent viral infections. • Analysis of the best animal models for testing enzymes for HBV, HSV, HIV and HPV. • Challenges facing in vivo delivery of therapeutic enzymes for persistent viral infections. • Safety issues to be addressed with proper animal studies.

  2. Advance in Researches on DNA Barcoding%植物DNA条形码研究进展

    Institute of Scientific and Technical Information of China (English)

    鲁松

    2012-01-01

    DNA barcoding is a new life identification system which can distinguish species rapidly and accurately by analyzing standard short and easy amplying DNA sequences with enough variation.In order to promote the development of domestic studies in plant DNA barcoding and taxonomy,this paper deals with DNA barcoding screening,application,present studying status in China,challenges and future prospects for plant DNA barcoding development.%DNA条形码技术是利用标准的、具有足够变异的、易扩增且相对较短的DNA片段在物种内的特异性和种间的多样性而创建的一种新的生物身份识别系统,从而实现对物种的快速自动鉴定。本文从植物DNA条形码的开发、应用、国内研究现状、植物DNA条形码面临的挑战以及发展前景等进行了综合分析,以期推动我国植物DNA条形码和分类学研究的发展。

  3. Recent advances in ancient DNA research and their implications for archaeobotany

    DEFF Research Database (Denmark)

    Brown, Terence A.; Cappellini, Enrico; Kistler, Logan;

    2015-01-01

    The scope and ambition of biomolecular archaeology is undergoing rapid change due to the development of new ‘next generation’ sequencing (NGS) methods for analysis of ancient DNA in archaeological specimens. These methods have not yet been applied extensively to archaeobotanical material but their...... utility has been demonstrated with desiccated, waterlogged and charred remains. The future use of NGS is likely to open up new areas of investigation that have been difficult or impossible with the traditional approach to aDNA sequencing. Species identification should become more routine with...

  4. Flavonoids acting on DNA topoisomerases: recent advances and future perspectives in cancer therapy.

    Science.gov (United States)

    Russo, P; Del Bufalo, A; Cesario, A

    2012-01-01

    Flavonoids, secondary metabolites ubiquitously produced in the plant kingdom, are low molecular weight polyphenolic molecules. They are characterized by variable chemical structures and show a vast array of biological activities (i.e... antiviral, antiinflammatory, antitumor, antimicrobial, estrogenic, antiestrogenic, antioxidant, mutagenic and antimutagenic) targeting different pathways. Some of these compounds such as Genistein, Daidzein or its synthetic derivative Phenoxodiol as well as Luteolin and Quercetin are able to inhibit DNA topoisomerases. This review discusses that Flavonoids targeting DNA topoisomerases may lead to novel drug development with anticancer potential. PMID:22998568

  5. ADVANCES OF DNA BARCODING%DNA条形码研究进展

    Institute of Scientific and Technical Information of China (English)

    王刚; 董言德; 赵彤言

    2014-01-01

    DNA barcodes technology is a new species identification methods , it is the combination of molecular biology and bioinformatics.In recent years, the technology has become a compelling focus of taxonomy research .In theory, DNA barcodes have been shown to have a very important role in the taxonomic identification, and to promote the development of a series of related disciplines, but different taxonomists hold different views. This paper reviews the origins , the development, operating principles and application of DNA barcode in classification, and outlines the possible problem of DNA barcodes in species classification.%DNA条形码( DNA Barcoding )技术是一种新的物种识别方法,它是分子生物学和生物信息学相结合的产物。在最近几年里,该技术已成为生物分类学中引人注目的研究热点。这一概念认为,类似于商店里使用扫描仪读取条形码,对地球上每一种生物通过快速分析其DNA中的一段基因(线粒体细胞色素c氧化酶Ⅰ亚基, mt COⅠ)加以识别。理论上, DNA条形码已被证明在生物分类鉴定中具有非常重要的作用,并推动了一系列相关学科的发展,但目前不同分类学家对其持的意见也不尽相同。本文综述了DNA条形码技术的产生、发展概况、原理与操作及其在分类中的应用,并概括了DNA条形码在应用于物种分类中可能存在的问题。

  6. Molecular Modeling and Chemoinformatics to Advance the Development of Modulators of Epigenetic Targets: A Focus on DNA Methyltransferases.

    Science.gov (United States)

    Prieto-Martínez, F D; Peña-Castillo, A; Méndez-Lucio, O; Fernández-de Gortari, E; Medina-Franco, J L

    2016-01-01

    In light of the emerging field of Epi-informatics, ie, computational methods applied to epigenetic research, molecular docking, and dynamics, pharmacophore and activity landscape modeling and QSAR play a key role in the development of modulators of DNA methyltransferases (DNMTs), one of the major epigenetic target families. The increased chemical information available for modulators of DNMTs has opened up the avenue to explore the epigenetic relevant chemical space (ERCS). Herein, we discuss recent progress on the identification and development of inhibitors of DNMTs as potential epi-drugs and epi-probes that have been driven by molecular modeling and chemoinformatics methods. We also survey advances on the elucidation of their structure-activity relationships and exploration of ERCS. Finally, it is illustrated how computational approaches can be applied to identify modulators of DNMTs in food chemicals. PMID:27567482

  7. Circulating Cell-Free DNA in Plasma of Locally Advanced Rectal Cancer Patients Undergoing Preoperative Chemoradiation: A Potential Diagnostic Tool for Therapy Monitoring

    Directory of Open Access Journals (Sweden)

    Matthias Zitt

    2008-01-01

    Full Text Available Circulating cell-free DNA opens up an interesting field for therapy monitoring, in particular during multimodal therapy protocols. The objective of this proof of principle study was to evaluate whether the amount of circulating plasma DNA has the potential to serve as a marker for therapy monitoring during the treatment course of locally advanced rectal cancer patients. We especially focused on kinetics of circulating DNA to assess whether variances in kinetics have the potential to discriminate between therapy responders and nonresponders.

  8. Advanced Electrochemical Platforms for Cancer Diagnostics based on Nanoswitchable DNA Architectures

    DEFF Research Database (Denmark)

    Ferapontova, Elena

    availability of screening tests, since any cancer is easier to treat when treatment is started early. In this context, genosensor nanotechnologies have become increasingly important for prognosis and diagnosis of cancer, post-cytotoxic therapy analysis, and anticancer drug development. Assays for mutated genes......Cancer is an important chronic disease and a serious public health problem. One in three can be expected to be diagnosed with cancer in our lifetimes and one in four will die of it. One of the most important factors in the fight against cancer is its early and reliable detection and greater...... and specific proteins, shown to be indicators of cancer development, are of high priority. Great efforts are made to develop new nanobiotechnologies to improve the selectivity and sensitivity of analysis. Among them, combination of electrochemistry and DNA nanotechnology allowed the development of...

  9. DNA methylation profiling in doxorubicin treated primary locally advanced breast tumours identifies novel genes associated with survival and treatment response

    Directory of Open Access Journals (Sweden)

    Børresen-Dale Anne-Lise

    2010-03-01

    Full Text Available Abstract Background Breast cancer is the most frequent cancer in women and consists of a heterogeneous collection of diseases with distinct histopathological, genetic and epigenetic characteristics. In this study, we aimed to identify DNA methylation based biomarkers to distinguish patients with locally advanced breast cancer who may benefit from neoadjuvant doxorubicin treatment. Results We investigated quantitatively the methylation patterns in the promoter regions of 14 genes (ABCB1, ATM, BRCA1, CDH3, CDKN2A, CXCR4, ESR1, FBXW7, FOXC1, GSTP1, IGF2, HMLH1, PPP2R2B, and PTEN in 75 well-described pre-treatment samples from locally advanced breast cancer and correlated the results to the available clinical and molecular parameters. Six normal breast tissues were used as controls and 163 unselected breast cancer cases were used to validate associations with histopathological and clinical parameters. Aberrant methylation was detected in 9 out of the 14 genes including the discovery of methylation at the FOXC1 promoter. Absence of methylation at the ABCB1 promoter correlated with progressive disease during doxorubicin treatment. Most importantly, the DNA methylation status at the promoters of GSTP1, FOXC1 and ABCB1 correlated with survival, whereby the combination of methylated genes improved the subdivision with respect to the survival of the patients. In multivariate analysis GSTP1 and FOXC1 methylation status proved to be independent prognostic markers associated with survival. Conclusions Quantitative DNA methylation profiling is a powerful tool to identify molecular changes associated with specific phenotypes. Methylation at the ABCB1 or GSTP1 promoter improved overall survival probably due to prolonged availability and activity of the drug in the cell while FOXC1 methylation might be a protective factor against tumour invasiveness. FOXC1 proved to be general prognostic factor, while ABCB1 and GSTP1 might be predictive factors for the response

  10. Overexpression of inhibitor of DNA-binding (ID)-1 protein related to angiogenesis in tumor advancement of ovarian cancers

    International Nuclear Information System (INIS)

    The inhibitor of DNA-binding (ID) has been involved in cell cycle regulation, apoptosis and angiogenesis. This prompted us to study ID functions in tumor advancement of ovarian cancers. Sixty patients underwent surgery for ovarian cancers. In ovarian cancers, the levels of ID-1, ID-2 and ID-3 mRNAs were determined by real-time reverse transcription-polymerase chain reaction. The histoscore with the localization of ID-1 was determined by immunohistochemistry. Patient prognosis was analyzed with a 36-month survival rate. Microvessel counts were determined by immunohistochemistry for CD34 and factor VIII-related antigen. ID-1 histoscores and mRNA levels both significantly (p < 0.001) increased in ovarian cancers according to clinical stage, regardless of histopathological type. Furthermore, 30 patients with high ID-1 expression had a lower survival rate (53%) compared to patients with low ID-1 expression (80%). ID-1 histoscores and mRNA levels significantly (p < 0.0001) correlated with microvessel counts in ovarian cancers. ID-1 increased in ovarian cancer cells during tumor progression. Moreover, ID-1 expression levels correlated with microvessel counts. Therefore, ID-1 might work on tumor advancement via angiogenesis and is considered to be a candidate for a prognostic indicator in ovarian cancers

  11. Concordance of Hypermethylated DNA and the Tumor Markers CA 15-3, CEA, and TPA in Serum during Monitoring of Patients with Advanced Breast Cancer

    DEFF Research Database (Denmark)

    Kristiansen, Søren; Jørgensen, Lars Mønster; Høgh Hansen, Morten;

    2015-01-01

    The serological protein tumor markers CA 15-3, CEA, and TPA are frequently used to monitor tumor burden among metastatic breast cancer patients. Breast cancer is associated with global DNA hypomethylation and hypermethylation of some promoter regions. No monitoring study has yet investigated the...... interrelationship between protein tumor markers, the global DNA hypomethylation, and hypermethylated genes in serum from patients with advanced disease. Twenty-nine patients with histologically proven advanced breast cancer received first-line chemotherapy with epirubicin. Samples were collected prior to each...... treatment and prospectively analyzed for CA 15-3, CEA, and TPA. The same samples were retrospectively analyzed for the concentration of hypermethylated RASSF1A and for global DNA hypomethylation using LINE-1. Among patients with elevated concentrations of the protein markers, concordance could be observed...

  12. Mammalian TIMELESS is involved in period determination and DNA damage-dependent phase advancing of the circadian clock.

    Directory of Open Access Journals (Sweden)

    Erik Engelen

    Full Text Available The transcription/translation feedback loop-based molecular oscillator underlying the generation of circadian gene expression is preserved in almost all organisms. Interestingly, the animal circadian clock proteins CRYPTOCHROME (CRY, PERIOD (PER and TIMELESS (TIM are strongly conserved at the amino acid level through evolution. Within this evolutionary frame, TIM represents a fascinating puzzle. While Drosophila contains two paralogs, dTIM and dTIM2, acting in clock/photoreception and chromosome integrity/photoreception respectively, mammals contain only one TIM homolog. Whereas TIM has been shown to regulate replication termination and cell cycle progression, its functional link to the circadian clock is under debate. Here we show that RNAi-mediated knockdown of TIM in NIH3T3 and U2OS cells shortens the period by 1 hour and diminishes DNA damage-dependent phase advancing. Furthermore, we reveal that the N-terminus of TIM is sufficient for interaction with CRY1 and CHK1 as well for homodimerization, and the C-terminus is necessary for nuclear localization. Interestingly, the long TIM isoform (l-TIM, but not the short (s-TIM, interacts with CRY1 and both proteins can reciprocally regulate their nuclear translocation in transiently transfected COS7 cells. Finally, we demonstrate that co-expression of PER2 abolishes the formation of the TIM/CRY1 complex through affinity binding competition to the C-terminal tail of CRY1. Notably, the presence of the latter protein region evolutionarily and structurally distinguishes mammalian from insect CRYs. We propose that the dynamic interaction between these three proteins could represent a post-translational aspect of the mammalian circadian clock that is important for its pace and adaption to external stimuli, such as DNA damage and/or light.

  13. DNA Repair by Reversal of DNA Damage

    OpenAIRE

    Yi, Chengqi; He, Chuan

    2013-01-01

    Endogenous and exogenous factors constantly challenge cellular DNA, generating cytotoxic and/or mutagenic DNA adducts. As a result, organisms have evolved different mechanisms to defend against the deleterious effects of DNA damage. Among these diverse repair pathways, direct DNA-repair systems provide cells with simple yet efficient solutions to reverse covalent DNA adducts. In this review, we focus on recent advances in the field of direct DNA repair, namely, photolyase-, alkyltransferase-,...

  14. An enzyme-free and resettable platform for the construction of advanced molecular logic devices based on magnetic beads and DNA.

    Science.gov (United States)

    Zhang, Siqi; Wang, Kun; Huang, Congcong; Li, Zhenyu; Sun, Ting; Han, De-Man

    2016-08-25

    A series of multiple logic circuits based on magnetic beads and DNA are constructed to perform resettable nonarithmetic functions, including a digital comparator, 4-to-2 encoder and 2-to-3 decoder, 2-to-1 encoder and 1-to-2 decoder. The signal reporter is composed of a G-quadruplex/NMM complex and a AuNP-surface immobilized molecular beacon. It is the first time that the designed DNA-based nonarithmetic nanodevices can share the same DNA platform with a reset function, which has great potential application in information processing at the molecular level. Another novel feature of the designed system is that the developed nanodevices are operated on a simple DNA/magnetic bead platform and share a constant threshold setpoint without the assistance of any negative logic conversion. The reset function is realized by heating the output system and the magnetic separation of the computing modules. Due to the biocompatibility and design flexibility of DNA, these investigations may provide a new route towards the development of resettable advanced logic circuits in biological and biomedical fields. PMID:27524500

  15. BRAF Mutation Testing in Cell-Free DNA from the Plasma of Patients with Advanced Cancers Using a Rapid, Automated Molecular Diagnostics System.

    Science.gov (United States)

    Janku, Filip; Huang, Helen J; Claes, Bart; Falchook, Gerald S; Fu, Siqing; Hong, David; Ramzanali, Nishma M; Nitti, Giovanni; Cabrilo, Goran; Tsimberidou, Apostolia M; Naing, Aung; Piha-Paul, Sarina A; Wheler, Jennifer J; Karp, Daniel D; Holley, Veronica R; Zinner, Ralph G; Subbiah, Vivek; Luthra, Rajyalakshmi; Kopetz, Scott; Overman, Michael J; Kee, Bryan K; Patel, Sapna; Devogelaere, Benoit; Sablon, Erwin; Maertens, Geert; Mills, Gordon B; Kurzrock, Razelle; Meric-Bernstam, Funda

    2016-06-01

    Cell-free (cf) DNA from plasma offers an easily obtainable material for BRAF mutation analysis for diagnostics and response monitoring. In this study, plasma-derived cfDNA samples from patients with progressing advanced cancers or malignant histiocytosis with known BRAF(V600) status from formalin-fixed paraffin-embedded (FFPE) tumors were tested using a prototype version of the Idylla BRAF Mutation Test, a fully integrated real-time PCR-based test with turnaround time about 90 minutes. Of 160 patients, BRAF(V600) mutations were detected in 62 (39%) archival FFPE tumor samples and 47 (29%) plasma cfDNA samples. The two methods had overall agreement in 141 patients [88%; κ, 0.74; SE, 0.06; 95% confidence interval (CI), 0.63-0.85]. Idylla had a sensitivity of 73% (95% CI, 0.60-0.83) and specificity of 98% (95% CI, 0.93-1.00). A higher percentage, but not concentration, of BRAF(V600) cfDNA in the wild-type background (>2% vs. ≤ 2%) was associated with shorter overall survival (OS; P = 0.005) and in patients with BRAF mutations in the tissue, who were receiving BRAF/MEK inhibitors, shorter time to treatment failure (TTF; P = 0.001). Longitudinal monitoring demonstrated that decreasing levels of BRAF(V600) cfDNA were associated with longer TTF (P = 0.045). In conclusion, testing for BRAF(V600) mutations in plasma cfDNA using the Idylla BRAF Mutation Test has acceptable concordance with standard testing of tumor tissue. A higher percentage of mutant BRAF(V600) in cfDNA corresponded with shorter OS and in patients receiving BRAF/MEK inhibitors also with shorter TTF. Mol Cancer Ther; 15(6); 1397-404. ©2016 AACR. PMID:27207774

  16. Recent advances in targeting the telomeric G-quadruplex DNA sequence with small molecules as a strategy for anticancer therapies.

    Science.gov (United States)

    Islam, Mohammad K; Jackson, Paul Jm; Rahman, Khondaker M; Thurston, David E

    2016-07-01

    Human telomeric DNA (hTelo), present at the ends of chromosomes to protect their integrity during cell division, comprises tandem repeats of the sequence d(TTAGGG) which is known to form a G-quadruplex secondary structure. This unique structural formation of DNA is distinct from the well-known helical structure that most genomic DNA is thought to adopt, and has recently gained prominence as a molecular target for new types of anticancer agents. In particular, compounds that can stabilize the intramolecular G-quadruplex formed within the human telomeric DNA sequence can inhibit the activity of the enzyme telomerase which is known to be upregulated in tumor cells and is a major contributor to their immortality. This provides the basis for the discovery and development of small molecules with the potential for selective toxicity toward tumor cells. This review summarizes the various families of small molecules reported in the literature that have telomeric quadruplex stabilizing properties, and assesses the potential for compounds of this type to be developed as novel anticancer therapies. A future perspective is also presented, emphasizing the need for researchers to adopt approaches that will allow the discovery of molecules with more drug-like properties in order to improve the chances of lead molecules reaching the clinic in the next decade. PMID:27442231

  17. Second-generation non-invasive high-throughput DNA sequencing technology in the screening of Down's syndrome in advanced maternal age women

    Science.gov (United States)

    ZHANG, JIAO; ZHANG, BIN

    2016-01-01

    The aim of the present study was to evaluate the efficacy of using non-invasive DNA testing technology in screening Down's syndrome among women of advanced maternal age (AMA) and to provide evidence for prenatal screening of Down's syndrome. With a double-blind design, 8 ml of peripheral venous blood samples were collected from 87 women aged ≥35 years after 12 weeks of pregnancy. All cases were recorded with unique identification cards with clinical details and followed up until delivery. All the non-invasive prenatal testing results were confirmed by amniotic fluid fetal karyotyping (the gold standard of aneuploidy test), follow-up examination by neonatologists or neonatal blood karyotyping. The sensitivity, specificity and other indicators of non-invasive DNA testing technology were calculated based on the data of 87 women of AMA. Among the 87 women of AMA, 5 were cases with abnormal numbers of chromosomes (3 cases of trisomy 21, 1 case of trisomy 18 and 1 case of 47, XXX). The sensitivity and specificity reached 100% for trisomy 21, trisomy 18 and 47, XXX. The present study supports that non-invasive DNA testing is a useful method of AMA screening of Down's syndrome with 100% accuracy. Therefore, it can be used as an important alternative screening method for Down's syndrome in women of AMA. PMID:27313855

  18. Increased Levels of Plasma Epstein Barr Virus DNA Identify a Poor-Risk Subset of Patients With Advanced Stage Cutaneous T-Cell Lymphoma

    Science.gov (United States)

    Haverkos, Bradley M.; Gru, Alejandro A.; Geyer, Susan M.; Bingman, Anissa K.; Hemminger, Jessica A.; Mishra, Anjali; Wong, Henry K.; Pancholi, Preeti; Freud, Aharon G.; Caligiuri, Michael A.; Baiocchi, Robert A.; Porcu, Pierluigi

    2016-01-01

    Discovering prognostic factors that simultaneously describe tumor characteristics and improve risk stratification is a priority in cutaneous T-cell lymphoma (CTCL). More than a third of advanced stage CTCL patients in this cohort had detectable cell free plasma Epstein–Barr virus (EBV)-DNA (pEBVd) using quantitative real-time polymerase chain reaction. An increased level of pEBVd was highly concordant with EBV (ie, Epstein–Barr virus RNAs) in tumor tissue and was associated with inferior survival. Introduction Outcomes in advanced stage (AS) cutaneous T-cell lymphomas (CTCL) are poor but with great variability. Epstein–Barr virus (EBV) is associated with a subset of non-Hodgkin lymphomas. Frequency of plasma EBV-DNA (pEBVd) detection, concordance with EBV RNA (EBER) in tumor tissue, codetection of plasma cytomegalovirus DNA (pCMVd), and prognostic effect in AS CTCL are unknown. Patients and Methods Patients (n = 46; 2006–2013) with AS CTCL (≥IIB) were retrospectively studied. pEBVd and pCMVd were longitudinally measured using quantitative real-time polymerase chain reaction. EBER in situ hybridization (ISH) was performed on tumor samples. Survival from time of diagnosis (ToD) and time of progression to AS was assessed. Results Plasma EBV-DNA and pCMVd were detected in 37% (17 of 46) and 17% (8 of 46) of AS CTCL patients, respectively. pCMVd detection was significantly more frequent in pEBVd-positive (pEBVd+) than pEBVd− patients (35% vs. 7%; P = .038). Tumor tissue for EBER-ISH was available in 14 of 17 pEBVd+ and 22 of 29 pEBVd− patients; 12 of 14 (85.7%) pEBVd+ patients were EBER+ versus 0 of 22 pEBVd− patients. Frequency of large cell transformation (LCT) tended to be greater in pEBVd+ patients, but was not significant (10 of 14 pEBVd+ vs. 10 of 23 pEBVd−; P = .17). No notable differences in rates of increased levels of serum lactate dehydrogenase (LDH) were observed (17 of 17 pEBVd+ vs. 27 of 29 pEBVd−). pEBVd detection was associated with

  19. Remote Activation of Host Cell DNA Synthesis in Uninfected Cells Signaled by Infected Cells in Advance of Virus Transmission

    OpenAIRE

    Schmidt, Nora; Hennig, Thomas; Remigiusz A Serwa; Marchetti, Magda; O'Hare, Peter

    2015-01-01

    ABSTRACT Viruses modulate cellular processes and metabolism in diverse ways, but these are almost universally studied in the infected cell itself. Here, we study spatial organization of DNA synthesis during multiround transmission of herpes simplex virus (HSV) using pulse-labeling with ethynyl nucleotides and cycloaddition of azide fluorophores. We report a hitherto unknown and unexpected outcome of virus-host interaction. Consistent with the current understanding of the single-step growth cy...

  20. Monitoring of epidermal growth factor receptor tyrosine kinase inhibitor-sensitizing and resistance mutations in the plasma DNA of patients with advanced non-small cell lung cancer during treatment with erlotinib

    DEFF Research Database (Denmark)

    Sorensen, Boe S; Wu, Lin; Wei, Wen; Tsai, Julie; Weber, Britta; Nexo, Ebba; Meldgaard, Peter

    2014-01-01

    was tested in plasma DNA from patients with advanced NSCLC with allele-specific polymerase chain reaction assays. Blood samples from 23 patients with adenocarcinoma of NSCLC that carried tyrosine kinase inhibitor-sensitizing EGFR mutations were taken immediately before treatment with erlotinib......BACKGROUND: The feasibility of monitoring epidermal growth factor receptor (EGFR) mutations in plasma DNA from patients with advanced non-small cell lung cancer (NSCLC) during treatment with erlotinib and its relation to disease progression was investigated. METHODS: The amount of EGFR-mutant DNA....... Additional blood samples were taken at timed intervals until erlotinib treatment was withdrawn. RESULTS: The amount of plasma DNA with sensitizing EGFR mutations was found to be reduced after the first cycle of erlotinib treatment in 22 of 23 patients (96%). No patients presented with the resistant T790M...

  1. Quantification and dynamic monitoring of EGFR T790M in plasma cell-free DNA by digital PCR for prognosis of EGFR-TKI treatment in advanced NSCLC.

    Directory of Open Access Journals (Sweden)

    Zhijie Wang

    Full Text Available BACKGROUND: Among advanced non-small cell lung cancer (NSCLC patients with an acquired resistance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKI, about 50% carry the T790M mutation, but this frequency in EGFR-TKI-naïve patients and dynamic change during therapy remains unclear. This study investigated the quantification and dynamic change of T790M mutation in plasma cell-free DNA (cf-DNA of advanced NSCLC patients to assess the clinical outcomes of EGFR-TKI therapy. MATERIALS AND METHODS: We retrospectively investigated 135 patients with advanced NSCLC who obtained progression-free survival (PFS after EGFR-TKI for >6 months for their EGFR sensitive mutations and T790M mutation in matched pre- and post-TKI plasma samples, using denaturing high-performance liquid chromatography (DHPLC, amplification refractory mutation system (ARMS, and digital-PCR (D-PCR. Real-time PCR was performed to measure c-MET amplification. RESULTS: Detection limit of D-PCR in assessing the T790M mutation was approximately 0.03%. D-PCR identified higher frequency of T790M than ARMS in pre-TKI (31.3% vs. 5.5% and post-TKI (43.0% vs. 25.2% plasma samples. Patients with pre-TKI T790M showed inferior PFS (8.9 vs. 12.1 months, p = 0.007 and overall survival (OS, 19.3 vs. 31.9 months, p = 0.001 compared with those without T790M. In patients harboring EGFR sensitive mutation, high quantities of pre-TKI T790M predicted poorer PFS (p = 0.001 on EGFR-TKI than low ones. Moreover, patients who experienced increased quantity of T790M during EGFR-TKI treatment showed superior PFS and OS compared with those with decreased changes (p = 0.044 and p = 0.015, respectively. CONCLUSION: Qualitative and quantitative T790M in plasma cf-DNA by D-PCR provided a non-invasive and sensitive assay to predict EGFR-TKI prognosis.

  2. Advances on DNA barcoding in fungi%真菌DNA条形码技术研究进展

    Institute of Scientific and Technical Information of China (English)

    周均亮; 赵瑞琳

    2013-01-01

    DNA条形码(DNA barcoding)技术作为一门新兴的物种鉴定方法以其灵敏、精确、方便和客观的优势,在动植物和微生物的分类鉴定中已经得到广泛应用.真菌鉴定中常用作标准条形码的是核核糖体DNA内转录间隔区(Internal transcribed spacer,ITS),如今也有一些新型条形码被发现和应用到实际操作中,如微条形码、ND6、EF3.本文对DNA条形码技术的产生和发展做出了总结,通过研究其在真菌中应用的实际案例分析了DNA条形码技术的优缺点及发展趋势,并指出DNA条形码技术将以全新的视角来弥补传统分类学的不足,最终实现生物自身的序列变异信息与现有形态分类学的结合.%As an emerging organism identification method,DNA barcoding has been widely used in plants,animals and microorganisms for its advantage of higher sensitivity,accuracy,and objectivity.Even the nuclear ribosomal internal transcribed spacer (ITS) is used as a standard barcode in fungal identification frequently,nowadays,there are more and more newbarcodes,such as the microcoding,ND6 and EF3.In this article we summarized the generation and developing history of DNA barcoding,also we present the advantage,shortcomings and the development trend based on fungal barcoding case studies.We indicated that DNA barcoding technique will be a good supplementary to the traditional morphology-based taxonomy,and towards a combination of natural evolutional relationships and morphological taxonomy in fungi.

  3. Advanced purification strategy for CueR, a cysteine containing copper(I) and DNA binding protein.

    Science.gov (United States)

    Balogh, Ria K; Gyurcsik, Béla; Hunyadi-Gulyás, Éva; Christensen, Hans E M; Jancsó, Attila

    2016-07-01

    Metal ion regulation is essential for living organisms. In prokaryotes metal ion dependent transcriptional factors, the so-called metalloregulatory proteins play a fundamental role in controlling the concentration of metal ions. These proteins recognize metal ions with an outstanding selectivity. A detailed understanding of their function may be exploited in potential health, environmental and analytical applications. Members of the MerR protein family sense a broad range of mostly late transition and heavy metal ions through their cysteine thiolates. The air sensitivity of latter groups makes the expression and purification of such proteins challenging. Here we describe a method for the purification of the copper-regulatory CueR protein under optimized conditions. In order to avoid protein precipitation and/or eventual aggregation and to get rid of the co-purifying Escherichia coli elongation factor, our procedure consisted of four steps supplemented by DNA digestion. Subsequent anion exchange on Sepharose FF Q 16/10, affinity chromatography on Heparin FF 16/10, second anion exchange on Source 30 Q 16/13 and gel filtration on Superdex 75 26/60 resulted in large amounts of pure CueR protein without any affinity tag. Structure and functionality tests performed with mass spectrometry, circular dichroism spectroscopy and electrophoretic gel mobility shift assays approved the success of the purification procedure. PMID:27038857

  4. Research Advances: DNA Computing Targets West Nile Virus, Other Deadly Diseases, and Tic-Tac-Toe; Marijuana Component May Offer Hope for Alzheimer's Disease Treatment; New Wound Dressing May Lead to Maggot Therapy--Without the Maggots

    Science.gov (United States)

    King, Angela G.

    2007-01-01

    This article presents three reports of research advances. The first report describes a deoxyribonucleic acid (DNA)-based computer that could lead to faster, more accurate tests for diagnosing West Nile Virus and bird flu. Representing the first "medium-scale integrated molecular circuit," it is the most powerful computing device of its type to…

  5. 植物DNA条形码研究进展%Current advances of DNA barcoding study in plants

    Institute of Scientific and Technical Information of China (English)

    宁淑萍; 颜海飞; 郝刚; 葛学军

    2008-01-01

    DNA条形码(DNA barcoding)已成为近5年来国际上生物多样性研究的热点,即通过使用短的标准DNA片段,对物种进行快速、准确的识别和鉴定.该技术在动物研究中已得到广泛的应用,所采用的标准片段是线粒体COI基因中约650 bp长的一段.然而在植物中DNA条形码的研究进展相对缓慢,目前尚处于对所提议的各片段比较和评价阶段,还未获得一致的标准片段.由于植物中线粒体基因组进化速率较慢,因此条形码片段主要在叶绿体基因组上进行选择,被提议的编码基因片段主要有rpoB,rpoCI,matK,rbcL,UPA,非编码区片段有tmH-psbA,atpF-atpH,psbK-psbI,此外还有核基因ITS.已有的研究表明以上任何一个单片段都不足以区分所有植物物种,因而不同的研究组相继提出了不同的片段组合方案,目前被广泛讨论的组合主要有5种.本文综述了DNA条形码序列的优点、标准、工作流程、分析方法和存在的争议,重点论述了植物条形码研究中被提议的各序列片段和组合的研究现状.

  6. DNA repair protocols

    DEFF Research Database (Denmark)

    Bjergbæk, Lotte

    In its 3rd edition, this Methods in Molecular Biology(TM) book covers the eukaryotic response to genomic insult including advanced protocols and standard techniques in the field of DNA repair. Offers expert guidance for DNA repair, recombination, and replication. Current knowledge of the mechanisms...... that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including...... recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly...

  7. Quantification of Cell-Free mSHOX2 Plasma DNA for Therapy Monitoring in Advanced Stage Non-Small Cell (NSCLC) and Small-Cell Lung Cancer (SCLC) Patients

    OpenAIRE

    Schmidt, Bernd; Beyer, Julia; Dietrich, Dimo; Bork, Ines; Liebenberg, Volker; Fleischhacker, Michael

    2015-01-01

    Purpose Most patients suffering from advanced lung cancer die within a few months. To exploit new therapy regimens we need better methods for the assessment of a therapy response. Material and Methods In a pilot study we prospectively enrolled 36 patients with advanced NSCLC and SCLC (34 stage IV, 2 stage IIIB) of whom 34 received standard platinum-based chemo/radiotherapy and two were treated with a tyrosine kinase inhibitor. We measured the levels of extracellular methylated SHOX2 DNA (mSHO...

  8. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

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

  9. 食物功能性成分对动物基因组 DNA 甲基化影响的研究进展%Research Advance on the Effect of Food Functional Components on Animal Genomic DNA Methylation

    Institute of Scientific and Technical Information of China (English)

    赵静; 李楠; 吴茹; 杨占威; 胡文兵; 王文君

    2016-01-01

    DNA methylation is one of the major epigenetic modifications in eukaryotic genomes, which can be influenced by certain food functional components, such as polyphenols, flavonoids, vitamin, n-3 polyunsaturated fatty acid etc. The effects of food functional components on DNA methylation are two-fold, either modulating the methyltransferase’s activity, and/or changing the number of methyl groups. Based upon the recent progress on the ongoing research, this paper expounds the effects and the possible mechanisms of a variety of functional components, i. e. , polyphenols, flavonoids, vitamin(folic acid, VB12, VB6), n-3 polyunsaturated fatty acid etc. , on the DNA methylation, which is expected to provide new ideas on exploring the molecular mechanisms of food functional components on DNA methylation modifications.%DNA 甲基化是表观遗传学的一部分。功能性成分如多酚、黄酮、维生素、n-3不饱和脂肪酸等对 DNA 甲基化有重要影响。功能性成分主要通过影响甲基转移酶活性和活性甲基基团数量实现对 DNA 甲基化的影响,结合研究成果阐述多种功能成分:多酚、黄酮、维生素(叶酸、VB12、VB6)、n-3多不饱和脂肪酸等对 DNA 甲基化的影响和作用机制进行综述,以期为从分子角度探究功能性成分的作用机理提供新思路。

  10. Interfacing DNA nanodevices with biology

    DEFF Research Database (Denmark)

    Vinther, Mathias; Kjems, Jørgen

    2016-01-01

    in biology and biomedicine acting as a molecular ‘nanorobot’ or smart drug interacting with the cellular machinery. In this review, we will explore and examine the perspective of DNA nanotechnology for such use. We summarize which requirements DNA nanostructures must fulfil to function in cellular...... environments and inside living organisms. In addition, we highlight recent advances in interfacing DNA nanostructures with biology....

  11. Next generation DNA led technologies

    CERN Document Server

    Jyothsna, G; Kashyap, Amita

    2016-01-01

    This brief highlights advances in DNA technologies and their wider applications. DNA is the source of life and has been studied since a generation, but very little is known as yet. Several sophisticated technologies of the current era have laid their foundations on the principle of DNA based mechanisms. DNA based technologies are bringing a new revolution of Advanced Science and Technology. Forensic Investigation, Medical Diagnosis, Paternity Disputes, Individual Identity, Health insurance, Motor Insurance have incorporated the DNA testing and profiling technologies for settling the issues.

  12. Research advance in noninvasive prenatal testing based on cell-free fetal DNA%基于胎儿游离DNA的无创产前检测的研究进展

    Institute of Scientific and Technical Information of China (English)

    张展; 赵小辰

    2016-01-01

    母血血浆中胎儿游离DNA( cffDNA)的发现为无创产前检测提供了新思路。虽然目前已经发现多种胎儿DNA标志物,但是如何准确地从母血血浆总游离DNA中区分出cffDNA对我们来说仍然是个难题。目前,基于cffDNA的无创产前检测已被用于多种疾病的检测和研究,随着技术的不断进步和发展,它将会有更广阔的应用前景。本文将从cffDNA的生物学特征、标志物,cffDNA的无创产前检测的临床应用及其现阶段存在的问题和发展前景等方面进行阐述。(中华检验医学杂志,2016,39:307-310)%The discovery of cell-free fetal DNA ( cffDNA) in maternal plasma provides a new idea for noninvasive prenatal testing( NIPT).Though some studies to date have shown several fetal DNA markers, how to accurately distinguish cffDNA from the pool of maternal plasma free DNA is still a challenge.So far, NIPT based on cffDNA has been used for detection and study of a variety of diseases, along with the advance and development of technology, it will have a more broad application prospects.This article will make a review for the research status from the biological characteristics and the markers of cffDNA, the clinical applications and the existing issues and development prospects of NIPT based on cffDNA.

  13. DNA in Nanoscale Electronics

    Science.gov (United States)

    Slinker, Jason

    2012-10-01

    DNA, the quintessential molecule of life, possesses a number of attractive properties for use in nanoscale circuits. Charge transport (CT) through DNA itself is of both fundamental and practical interest. Fundamentally, DNA has a unique configuration of π-stacked bases in a well ordered, double helical structure. Given its unparalleled importance to life processes and its arrangement of conjugated subunits, DNA has been a compelling target of conductivity studies. In addition, further understanding of DNA CT will elucidate the biological implications of this process and advance its use in sensing technologies. We have investigated the fundamentals of DNA CT by measuring the electrochemistry of DNA monolayers under biologically-relevant conditions. We have uncovered both fundamental kinetic parameters to distinguish between competing models of operation as well as the practical implications of DNA CT for sensing. Furthermore, we are leveraging our studies of DNA conductivity for the manufacture of nanoscale circuits. We are investigating the electrical properties and self-assembly of DNA nanowires containing artificial base pair surrogates, which can be prepared through low cost and high throughput automated DNA synthesis. This unique and economically viable approach will establish a new paradigm for the scalable manufacture of nanoscale semiconductor devices.

  14. DNA media storage

    Institute of Scientific and Technical Information of China (English)

    Christy M.Bogard; Eric C.Rouchka; Benjamin Arazi

    2008-01-01

    In 1994. University of Southern California computer scientist,Dr.Leonard Adleman solved the Hamiltonian path problem using DNA as a computational mechanism.He proved the principle that DNA computing could be used to solve computationally complex problems.Because of the limitations in discovery time,resource requirements,and sequence mismatches,DNA computing has not yet become a commonly accepted practice.However,advancements are continually being discovered that are evolving the field of DNA computing.Practical applications of DNA are not restricted to computation alone.This research presents a novel approach in which DNA could be used as a means of storing files.Through the use of multiple sequence alignment combined with intelligent heuristics,the most probabilistic file contents can be determined with minimal errors.

  15. Electrocatalysis in DNA Sensors.

    Science.gov (United States)

    Furst, Ariel; Hill, Michael G; Barton, Jacqueline K

    2014-12-14

    Electrocatalysis is often thought of solely in the inorganic realm, most often applied to energy conversion in fuel cells. However, the ever-growing field of bioelectrocatalysis has made great strides in advancing technology for both biofuel cells as well as biological detection platforms. Within the context of bioelectrocatalytic detection systems, DNA-based platforms are especially prevalent. One subset of these platforms, the one we have developed, takes advantage of the inherent charge transport properties of DNA. Electrocatalysis coupled with DNA-mediated charge transport has enabled specific and sensitive detection of lesions, mismatches and DNA-binding proteins. Even greater signal amplification from these platforms is now being achieved through the incorporation of a secondary electrode to the platform both for patterning DNA arrays and for detection. Here, we describe the evolution of this new DNA sensor technology. PMID:25435647

  16. The correlation between cell-free DNA and tumour burden was estimated by PET/CT in patients with advanced NSCLC

    DEFF Research Database (Denmark)

    Nygaard, A D; Holdgaard, Paw; Spindler, K-L G;

    2014-01-01

    -FDG) PET/computed tomography (CT) scan was performed and evaluated in terms of metabolic tumour volume (MTV) and total lesion glycolysis (TLG). Tumour contours were delineated semi-automatically by a threshold standardised uptake value (SUV) of 2.5. The primary end point was correlation among cfDNA, MTV...

  17. 线粒体DNA突变和疾病的关系研究进展%Advance in Research of Mitochondrial DNA Mutations in Human Diseases

    Institute of Scientific and Technical Information of China (English)

    于君; 高政南; 杨泽

    2008-01-01

    线粒体是细胞能量生成的场所,人类线粒体DNA(mtDNA)上有37个编码基因,其中有13个蛋白质基因,2个rRNA基因和22个tRNA基因.mtDNA突变是引起多因素疾病和部分遗传疾病的重要原因之一,本文就线粒体基因组学、mtDNA疾病模型,mtDNA疾病的临床特征以及mtDNA疾病的防治进展进行综述.

  18. LASER SCANNING CYTOMETRIC DNA ANALYSES AND EXPRE- SSION OF P53 PROTEIN,KI67 AND BCL-X IN EARLY AND ADVANCED CARCINOMAS OF THE VOCAL CORD

    Institute of Scientific and Technical Information of China (English)

    林梅绥; 金嘉平; 陈颖; 花井淳

    2003-01-01

    Objective To study DNA ploidy and genetic changes in the different stages of neoplastic growth in the vocal cord, as well as their biological behavior, for further recognition of the lesions of carcinoma in situ and early carcinoma. Methods 18 tumor lesions of the vocal cord were DNA analyzed by laser scanning cytometry and followed up, and 62 lesions were immunohistochemically investigated for p53, Ki67 and Bcl-X, and with main observation on carcinomas in situ (CISs) and early microinvasive carcinomas (EMICs) which were compared with invasive carcinomas and polyps. Results DNA analysis showed that almost all the CISs and EMICs were diploidy, while 90% invasive carcinomas were aneuploidy. Follow-up data displayed that no one died of the tumor in CIS and EMIC, as well as in the patients with diploidy tumor, and all the patients died of the tumors were with anueploidy tumor. Immunohistochemically, 86% of CIS and EMIC and 91% of invasive carcinoma expressed p53 protein, and the positivities for Ki67 in them were respectively 29% and 27%, which were very significantly different from those of polyps of the vocal cord(P<0. 001). In contrast, expression of Bcl-X were decreasing from benign to malignant lesions, and it was lowest in the invasive carcinomas, significantly different from that of polyp(P=0. 002). Conclusion The present study showed that there were differences of DNA ploidy and genetic expressions among benign lesions, CISs and EMICs, and invasive carcinomas of the vocal cord, indicating that they might be different in biological entities. CIS of the vocal cord could be considered as a borderline lesion, and is better to receive conservative treatment. Moreover, p53 protein determination combined with Ki67 would be helpful in diagnosis of the carcinomas of the vocal cord.

  19. DNA Book

    OpenAIRE

    Kawai, Jun; Hayashizaki, Yoshihide

    2003-01-01

    We propose herein a new method of DNA distribution, whereby DNA clones or PCR products are printed directly onto the pages of books and delivered to users along with relevant scientific information. DNA sheets, comprising water-soluble paper onto which DNA is spotted, can be bound into books. Readers can easily extract the DNA fragments from DNA sheets and amplify them using PCR. We show that DNA sheets can withstand various conditions that may be experienced during bookbinding and deli...

  20. Advances in DNA Extraction and Gene Detection for Vegetable Oils%植物油DNA提取和基因检测研究进展

    Institute of Scientific and Technical Information of China (English)

    齐玲倩; 刘秀; 丁梦璇; 刘远远; 柯润辉; 尹建军

    2016-01-01

    Methods for gene detection have been widely used in the authentication and GMO detection for vegetable oils because of their rapidity, efficiency, sensitivity and accuracy. While, as for vegetable oils, the low quantity and integrity of DNA caused by being refined increase the difficulties of DNA extraction and gene detection. In this paper, we review the progress of DNA extraction and gene detection for vegetable oils and make some respect for their future , so as to provide theoretical reference for the researchers in some degree.%基因检测方法以其快速、高效、灵敏、准确的特点而广泛应用在植物油真实性和转基因成分鉴定中。但植物油大都经过精制加工,DNA含量极少且完整度低,这对植物油的基因提取和检测造成了极大的困扰。本文对植物油DNA提取和基因检测进展进行了综述,并对以后的发展进行了展望,以期为研究者提供一定的理论参考。

  1. 植物油DNA提取和基因检测研究进展%Advances in DNA Extraction and Gene Detection for Vegetable Oils

    Institute of Scientific and Technical Information of China (English)

    齐玲倩; 刘秀; 丁梦璇; 刘远远; 柯润辉; 尹建军

    2016-01-01

    基因检测方法以其快速、高效、灵敏、准确的特点而广泛应用在植物油真实性和转基因成分鉴定中。但植物油大都经过精制加工,DNA含量极少且完整度低,这对植物油的基因提取和检测造成了极大的困扰。本文对植物油DNA提取和基因检测进展进行了综述,并对以后的发展进行了展望,以期为研究者提供一定的理论参考。%Methods for gene detection have been widely used in the authentication and GMO detection for vegetable oils because of their rapidity, efficiency, sensitivity and accuracy. While, as for vegetable oils, the low quantity and integrity of DNA caused by being refined increase the difficulties of DNA extraction and gene detection. In this paper, we review the progress of DNA extraction and gene detection for vegetable oils and make some respect for their future , so as to provide theoretical reference for the researchers in some degree.

  2. Cleaving DNA with DNA

    Science.gov (United States)

    Carmi, Nir; Balkhi, Shameelah R.; Breaker, Ronald R.

    1998-03-01

    A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This ``deoxyribozyme'' can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a kobs of 0.2 min-1, whereas the corresponding uncatalyzed reaction could not be detected. The duplex and triplex recognition domains can be altered, making possible the targeted cleavage of single-stranded DNAs with different nucleotide sequences. Several small synthetic DNAs were made to function as simple ``restriction enzymes'' for the site-specific cleavage of single-stranded DNA.

  3. Advancing forensic RNA typing: On non-target secretions, a nasal mucosa marker, a differential co-extraction protocol and the sensitivity of DNA and RNA profiling.

    Science.gov (United States)

    van den Berge, Margreet; Bhoelai, Bryan; Harteveld, Joyce; Matai, Anuska; Sijen, Titia

    2016-01-01

    The forensic identification of human body fluids and tissues by means of messenger RNA (mRNA) profiling is a long studied methodology that is increasingly applied to casework samples. Previously, we have described an mRNA multiplex system that targets blood, saliva, semen, menstrual secretion, vaginal mucosa and skin (Lindenbergh et al. and van den Berge et al.). In this study we consider various topics to improve this mRNA profiling system or its use and adapt the method accordingly. Bodily secretions that may be encountered at a crime scene whilst not targeted by the multiplex-id est nasal mucosa, sweat, tears, faeces and urine-were examined for false positive signals. The results prompted us to identify a nasal mucosa marker that allows the discrimination of nasal mucosa from saliva or vaginal mucosa and nosebleed blood from peripheral blood. An updated version of the multiplex was prepared to which the nasal mucosa marker was added and in which markers for semen, vaginal mucosa and blood were replaced. Lactobacillus markers were regarded unsuitable as replacement for vaginal mucosa mRNA markers because of background signals on penile swabs that appeared devoid of female DNA. Furthermore, we provide approaches to deal with highly unbalanced mixtures. First, a differential extraction protocol was incorporated into a co-extraction protocol to allow DNA and RNA analysis of separated non-sperm and sperm fractions. In a second approach, besides the standard multiplex, a customized multiplex is used which excludes markers for prevailing cell types. This allows the use of lower cDNA inputs for the prevailing cell types and higher inputs for cell types that appear masked. Additionally, we assessed the relation between the percentage of alleles or markers detected in DNA or RNA profiles when decreasing sample amounts are analysed. While blood, saliva, semen and menstrual secretion show the trend that DNA profiling is more sensitive than RNA profiling, the reverse is seen

  4. Advance in Human Circulating DNA at Critical Heart Attack%人体循环DNA在心脏危急症方面的研究进展

    Institute of Scientific and Technical Information of China (English)

    王敏; 郭延松

    2015-01-01

    血浆DNA和线粒体DNA是血液循环系统中游离状态的DNA.健康人的血液中含有极微量的循环DNA并维持相对恒定,当机体在病理状态时常有不同程度的升高.通过血浆DNA和线粒体DNA的实时监测,可以实现心肌梗死、心脏骤停等心脏危急症的早期诊断及预后评估.

  5. Epidermal growth factor receptor genotype in plasma DNA and outcome of chemotherapy in the Chinese patients with advanced non-small cell lung cancer

    Institute of Scientific and Technical Information of China (English)

    ZHUO Ming-lei; DUAN Jian-chun; WANG Yu-yan; GUO Qing-zhi; LIU Xu-yi; LIU Ning-hong; WANG Jie; WU Mei-na; ZHAO Jun; Sonya Wei Song; BAI Hua; WANG Shu-hang; YANG Lu; AN Tong-tong; WANG Xin

    2011-01-01

    Background The genotype of epidermal growth factor receptor (EGFR) is associated with tyrosine kinase inhibitor and effectiveness of therapy,but its role in cytotoxic chemotherapy is still unknown.Previous studies indicated that certain EGFR mutations were associated with response and progression free survival following platinum based chemotherapy.Our recent studies have identified that EGFR genotypes in the tumour tissues were not associated with response to the first-line chemotherapy in Chinese patients with advanced non-small cell lung cancer (NSCLC).In this study,we investigated associations of EGFR genotypes from plasma of patients with advanced NSCLC and response to first-line chemotherapy and prognosis.Methods We enrolled 145 advanced NSCLC patients who had received first-line chemotherapy in our department.We examined plasma EGFR genotypes for these patients and associations of EGFR mutations with response to chemotherapy and clinical outcomes.Results There were 54 patients with known EGFR mutations and 91 cases of wild types.No significant difference was detected in the response rate to first-line chemotherapy between mutation carriers and wild-type patients (37.0% vs.31.9%).The median survival time and 1-,2-year survival rates were higher in mutation carriers than wild-types (24months vs.18 months,85.7% vs.65.7% and 43.7% vs.25.9%,P=0.047).Clinical stage (IV vs.Ⅲb),response to the first-line chemotherapy (partial vs.no) and EGFR genotype were independent prognostic factors.Conclusion Plasma EGFR mutations in the Chinese patients with advanced NSCLC is not a predictor for the response to first-line chemotherapy,but an independent prognostic factor indicating longer survival.

  6. Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma

    OpenAIRE

    Philip Burnham; Min Seong Kim; Sean Agbor-Enoh; Helen Luikart; Hannah A. Valantine; Kiran K Khush; Iwijn De Vlaminck

    2016-01-01

    Circulating cell-free DNA (cfDNA) is emerging as a powerful monitoring tool in cancer, pregnancy and organ transplantation. Nucleosomal DNA, the predominant form of plasma cfDNA, can be adapted for sequencing via ligation of double-stranded DNA (dsDNA) adapters. dsDNA library preparations, however, are insensitive to ultrashort, degraded cfDNA. Drawing inspiration from advances in paleogenomics, we have applied a single-stranded DNA (ssDNA) library preparation method to sequencing of cfDNA in...

  7. 线粒体DNA相关疾病的分子遗传学研究%Advances in molecular genetics in mitochondrial DNA-related diseases

    Institute of Scientific and Technical Information of China (English)

    孟洪弟; 吴希如

    2001-01-01

    @@ 在儿童退行性疾病中,诸如发育延迟、感觉运动障碍、惊厥、糖尿病以及器官衰竭等,线粒体功能紊乱是一个相当常见的病因[1].近年来线粒体DNA(mtDNA)突变及其致病作用也是一些晚发性疾病如Alzheimer's病、肿瘤及Parkinson's病的研究热点.据Finland的一项研究表明mtDNA相关疾病的发病率≥16.3/10万.自从1963年发现mtDNA和1988年首次报道致病性mtDNA突变以来,迄今已发现至少97个点突变和很多的mtDNA重排(缺失、重复),mtDNA突变业已成为线粒体疾病的重要病因之一[1,2].

  8. Role of DNA profiling in forensic odontology

    OpenAIRE

    S Leena Sakari; Sudha Jimson; K M K Masthan; Jenita Jacobina

    2015-01-01

    The recent advances in DNA profiling have made DNA evidence to be more widely accepted in courts. This has revolutionized the aspect of forensic odontology. DNA profiling/DNA fingerprinting has come a long way from the conventional fingerprints. DNA that is responsible for all the cell′s activities, yields valuable information both in the healthy and diseased individuals. When other means of traditional identification become impossible following mass calamities or fire explosions, teeth provi...

  9. DNA-Conjugated Organic Chromophores in DNA Stacking Interactions

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V.; Pedersen, Erik Bjerregaard

    2009-01-01

    Since the discovery of the intercalation of acridine derivatives into DNA (1961), chemists have synthesized many intercalators tethered to DNA. Advances in the chemical synthesis of modified nucleosides along with progress in oligonucleotide synthesis have made it possible to introduce organic...

  10. Quantification of cell-free mSHOX2 Plasma DNA for therapy monitoring in advanced stage non-small cell (NSCLC and small-cell lung cancer (SCLC patients.

    Directory of Open Access Journals (Sweden)

    Bernd Schmidt

    Full Text Available Most patients suffering from advanced lung cancer die within a few months. To exploit new therapy regimens we need better methods for the assessment of a therapy response.In a pilot study we prospectively enrolled 36 patients with advanced NSCLC and SCLC (34 stage IV, 2 stage IIIB of whom 34 received standard platinum-based chemo/radiotherapy and two were treated with a tyrosine kinase inhibitor. We measured the levels of extracellular methylated SHOX2 DNA (mSHOX2 in plasma before and during therapy until re-staging. The mSHOX2 analysis was blinded with respect to the clinical data making it an observational study.According to the re-staging of 31 first-line patients, 19 patients were classified as non-responders while 12 patients were in the responder group. We observed a tight correlation between radiological data and the change of plasma mSHOX2 level as the equivalent for a therapy response. A ROC analysis showed a high discriminatory power for both patient groups already one week after therapy start (AUC 0.844. Additionally, a Kaplan-Meier and Cox Proportional Hazards analyses revealed a strong relationship between survival and plasma mSHOX2 value p ≤ 0.001 (hazard ratio 11.08 providing some evidence for mSHOX2 also being a predictive marker.The longitudinal measurement of extracellular plasma mSHOX2 DNA yields information about the response to cytotoxic treatment and allows an early assessment of treatment response for lung cancer patients. If confirmed in a larger study this would be a valuable tool for selecting and guiding a cytotoxic treatment.

  11. Quantification of Cell-Free mSHOX2 Plasma DNA for Therapy Monitoring in Advanced Stage Non-Small Cell (NSCLC) and Small-Cell Lung Cancer (SCLC) Patients

    Science.gov (United States)

    Schmidt, Bernd; Beyer, Julia; Dietrich, Dimo; Bork, Ines; Liebenberg, Volker; Fleischhacker, Michael

    2015-01-01

    Purpose Most patients suffering from advanced lung cancer die within a few months. To exploit new therapy regimens we need better methods for the assessment of a therapy response. Material and Methods In a pilot study we prospectively enrolled 36 patients with advanced NSCLC and SCLC (34 stage IV, 2 stage IIIB) of whom 34 received standard platinum-based chemo/radiotherapy and two were treated with a tyrosine kinase inhibitor. We measured the levels of extracellular methylated SHOX2 DNA (mSHOX2) in plasma before and during therapy until re-staging. The mSHOX2 analysis was blinded with respect to the clinical data making it an observational study. Results According to the re-staging of 31 first-line patients, 19 patients were classified as non-responders while 12 patients were in the responder group. We observed a tight correlation between radiological data and the change of plasma mSHOX2 level as the equivalent for a therapy response. A ROC analysis showed a high discriminatory power for both patient groups already one week after therapy start (AUC 0.844). Additionally, a Kaplan-Meier and Cox Proportional Hazards analyses revealed a strong relationship between survival and plasma mSHOX2 value p≤0.001 (hazard ratio 11.08) providing some evidence for mSHOX2 also being a predictive marker. Conclusion The longitudinal measurement of extracellular plasma mSHOX2 DNA yields information about the response to cytotoxic treatment and allows an early assessment of treatment response for lung cancer patients. If confirmed in a larger study this would be a valuable tool for selecting and guiding a cytotoxic treatment. PMID:25675432

  12. Advances in the study of multivalent recombinant DNA vaccines utilizing the hepatitis B virus surface antigen gene%乙肝表面抗原载体多价重组核酸疫苗研究进展

    Institute of Scientific and Technical Information of China (English)

    肖婷; 郭根灵; 辛宪云; 魏庆宽

    2012-01-01

    研究表明,乙肝病毒的包膜蛋白HBsAg不仅可以作为疫苗的理想候选分子,还可作为基因工程疫苗的理想载体,用来成功构建多种重组核酸疫苗.本文概述了以乙肝表面抗原为载体,重组或联合其他病毒、寄生虫、细胞因子等其他基因制作多价核酸疫苗的研究进展.%Studies have shown that hepatitis B virus envelope protein HBsAg can be used as an ideal candidate molecule for vaccines and also as an ideal vehicle for genetically engineered vaccines to successfully build a variety of recombinant DNA vaccines. This article provides an overview of advances in recombinant DNA vaccines prepared by using hepatitis B virus surface antigen as a carrier to restructure or join it to other viruses, parasites, cell factors, or other genes.

  13. Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot.

    Directory of Open Access Journals (Sweden)

    W John Kress

    Full Text Available BACKGROUND: Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny. METHODOLOGY/PRINCIPAL FINDINGS: Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history. CONCLUSIONS/SIGNIFICANCE: As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community

  14. DNA supercoiling inhibits DNA knotting.

    OpenAIRE

    Burnier Y.; Dorier J.; Stasiak A.

    2008-01-01

    Despite the fact that in living cells DNA molecules are long and highly crowded, they are rarely knotted. DNA knotting interferes with the normal functioning of the DNA and, therefore, molecular mechanisms evolved that maintain the knotting and catenation level below that which would be achieved if the DNA segments could pass randomly through each other. Biochemical experiments with torsionally relaxed DNA demonstrated earlier that type II DNA topoisomerases that permit inter- and intramolecu...

  15. Advanced In vivo Use of CRISPR/Cas9 and Anti-sense DNA Inhibition for Gene Manipulation in the Brain

    Science.gov (United States)

    Walters, Brandon J.; Azam, Amber B.; Gillon, Colleen J.; Josselyn, Sheena A.; Zovkic, Iva B.

    2016-01-01

    Gene editing tools are essential for uncovering how genes mediate normal brain–behavior relationships and contribute to neurodegenerative and neuropsychiatric disorders. Recent progress in gene editing technology now allows neuroscientists unprecedented access to edit the genome efficiently. Although many important tools have been developed, here we focus on approaches that allow for rapid gene editing in the adult nervous system, particularly CRISPR/Cas9 and anti-sense nucleotide-based techniques. CRISPR/Cas9 is a flexible gene editing tool, allowing the genome to be manipulated in diverse ways. For instance, CRISPR/Cas9 has been successfully used to knockout genes, knock-in mutations, overexpress or inhibit gene activity, and provide scaffolding for recruiting specific epigenetic regulators to individual genes and gene regions. Moreover, the CRISPR/Cas9 system may be modified to target multiple genes at one time, affording simultaneous inhibition and overexpression of distinct genetic targets. Although many of the more advanced applications of CRISPR/Cas9 have not been applied to the nervous system, the toolbox is widely accessible, such that it is poised to help advance neuroscience. Anti-sense nucleotide-based technologies can be used to rapidly knockdown genes in the brain. The main advantage of anti-sense based tools is their simplicity, allowing for rapid gene delivery with minimal technical expertise. Here, we describe the main applications and functions of each of these systems with an emphasis on their many potential applications in neuroscience laboratories. PMID:26793235

  16. DNA vaccines

    OpenAIRE

    Coban, Cevayir; Kobiyama, Kouji; Jounai, Nao; Tozuka, Miyuki; Ishii, Ken J.

    2013-01-01

    Since the introduction of DNA vaccines two decades ago, this attractive strategy has been hampered by its low immunogenicity in humans. Studies conducted to improve the immunogenicity of DNA vaccines have shown that understanding the mechanism of action of DNA vaccines might be the key to successfully improving their immunogenicity. Our current understanding is that DNA vaccines induce innate and adaptive immune responses in two ways: (1) encoded protein (or polypeptide) antigen(s) by the DNA...

  17. Monitoring Biodiversity using Environmental DNA

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis

    . Finally, a study tests the applicability of non-destructive DNA extraction from old and ancient insect remains. DNA is successfully retrieved, amplified and equenced from dried museum beetle specimens up to 188 years old, ermafrost-preserved macrofossils up to 26.000 years old and directly from 1800......As any species interacts with its environment, most of them will at some point expel DNA to their surroundings. Such DNA can be picked up in environmental samples, isolated and analysed. Within the last decade, this has become a multidisciplinary research field known as Environmental DNA (eDNA......). Especially the advance in DNA sequencing technology has revolutionized this field and opened new frontiers in ecology, evolution and environmental sciences. Also, it is becoming a powerful tool for field biologist, with new and efficient methods for monitoring biodiversity. This thesis focuses on the use of...

  18. DNA damage tolerance.

    Science.gov (United States)

    Branzei, Dana; Psakhye, Ivan

    2016-06-01

    Accurate chromosomal DNA replication is fundamental for optimal cellular function and genome integrity. Replication perturbations activate DNA damage tolerance pathways, which are crucial to complete genome duplication as well as to prevent formation of deleterious double strand breaks. Cells use two general strategies to tolerate lesions: recombination to a homologous template, and trans-lesion synthesis with specialized polymerases. While key players of these processes have been outlined, much less is known on their choreography and regulation. Recent advances have uncovered principles by which DNA damage tolerance is regulated locally and temporally - in relation to replication timing and cell cycle stage -, and are beginning to elucidate the DNA dynamics that mediate lesion tolerance and influence chromosome structure during replication. PMID:27060551

  19. Recent advances in silage microbiology

    Science.gov (United States)

    Recent advances in our understanding of silage microbiology are reviewed. The ability to extract microbial DNA from silages, amplify portions of DNA, and use the amplified regions to identify strains of microorganisms is at the core of the changes occurring recently in silage microbiology. These dev...

  20. Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor

    International Nuclear Information System (INIS)

    Uracil N-glycosylase from M. tuberculosis has been crystallized in complex with a proteinaceous inhibitor (Ugi) and X-ray diffraction data have been collected. Uracil N-glycosylase is an enzyme which initiates the pathway of uracil-excision repair of DNA. The enzyme from Mycobacterium tuberculosis was co-expressed with a proteinaceous inhibitor from Bacillus subtilis phage and was crystallized in monoclinic space group C2, with unit-cell parameters a = 201.14, b = 64.27, c = 203.68 Å, β = 109.7°. X-ray data from the crystal have been collected for structure analysis

  1. DNA Methylation

    OpenAIRE

    Alokail, Majed S.; Alenad, Amal M

    2015-01-01

    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...

  2. DNA looping.

    OpenAIRE

    Matthews, K S

    1992-01-01

    DNA-looping mechanisms are part of networks that regulate all aspects of DNA metabolism, including transcription, replication, and recombination. DNA looping is involved in regulation of transcriptional initiation in prokaryotic operons, including ara, gal, lac, and deo, and in phage systems. Similarly, in eukaryotic organisms, the effects of enhancers appear to be mediated at least in part by loop formation, and examples of DNA looping by hormone receptor proteins and developmental regulator...

  3. Charge Transport in DNA - Insights from Simulations

    OpenAIRE

    Wolter, Mario

    2013-01-01

    Charge transport and charge transfer (CT) capabilities of deoxyribonucleic acid (DNA) are investigated. A QM/MM multi-scale framework is applied to calculate the CT capabilities of DNA under conditions resembling the experimental setup. The simulations are able to explain and predict the outcome of experiments and therefore make suggestions in advance. Based on the findings, suitable DNA sequences can be opted for the design of DNA-based devices as nano-scale electronic elements.

  4. DNA structure

    OpenAIRE

    Bowater, R

    2003-01-01

    Deoxyribonucleic acid (DNA) is a polymer of nucleotides. In the cell, DNA usually adopts a double-stranded helical form, with complementary base-pairing holding the two strands together. The most stable conformation is called B-form DNA, although other structures can occur under specific conditions.

  5. 局部晚期宫颈癌组织中 ERCC1 mRNA 表达及 DNA 倍体与新辅助化疗效果的关系%Relationship of expression of ERCC1 mRNA and DNA ploidy in locally advanced cervical cancer tissue to curative effect of neoadjuvant chemo-therapy

    Institute of Scientific and Technical Information of China (English)

    马一鸣; 陈红敏; 邓君丽; 阎夏; 窦萌萌; 王莉

    2014-01-01

    Aim:To explore relationship between the effect of neoadjuvant chemotherapy ( NACT) and the expression of ERCC1 mRNA,DNA ploidy in locally advanced cervical cancer ( LACC) tissue.Methods:A total of 60 cases of LACC biopsy specimens before chemotherapy were collected .PCR combined with the fluorescence probe technique were applied to analyze the expression of ERCC 1 mRNA in the specimens , and the DNA quantitative analysis technique was adopted to an-alyze DNA ploidy.Results:Thirty-three cases were effective in the 60 patients, and the effective rate was 55.0%.There was a correlation between ERCC1 mRNA expression, DNA ploidy and the curative effect of NACT(P<0.05).The result of logistic regression showed that high expression of ERCC 1 mRNA was a negative factor for curative effect of NACT [β=-2.672,OR(95%CI) =0.069 (0.008 -0.583)],and DNA diploid was a positive factor [β=1.348,OR(95%CI)=3.850(1.134-13.075)].Conclusion:The expression of ERCC1 mRNA and DNA ploidy in LACC tissue may be related to the sensitivity of NACT .%目的:探讨局部晚期宫颈癌( LACC)组织中ERCC1 mRNA表达和DNA倍体与新辅助化疗( NACT)敏感性的关系。方法:收集60例LACC患者NACT前宫颈活检标本,应用PCR结合实时荧光探针技术分析标本中ER-CC1 mRNA的表达情况,采用细胞DNA定量分析技术分析DNA倍体。结果:60例患者中NACT有效33例,有效率为55.0%。 LACC组织中ERCC1 mRNA表达水平、DNA倍体与NACT疗效有关( P<0.05);logistic回归模型分析结果也显示,LACC组织中ERCC1 mRNA高表达是NACT疗效的负性影响因素[β=-2.672,OR(95%CI)=0.069(0.008~0.583)], DNA二倍体则是正性影响因素[β=1.348,OR(95%CI)=3.850(1.134~13.075)]。结论:LACC组织中ERCC1、DNA倍体表达与NACT敏感性密切相关。

  6. Electrocatalysis in DNA sensors

    OpenAIRE

    Furst, Ariel; Hill, Michael G.; Barton, Jacqueline K.

    2014-01-01

    Electrocatalysis is often thought of solely in the inorganic realm, most often applied to energy conversion in fuel cells. However, the ever-growing field of bioelectrocatalysis has made great strides in advancing technology for both biofuel cells as well as biological detection platforms. Within the context of bioelectrocatalytic detection systems, DNA-based platforms are especially prevalent. One subset of these platforms, the one we have developed, takes advantage of the inherent charge tr...

  7. DNA Immunization

    OpenAIRE

    Wang, Shixia; Lu, Shan

    2013-01-01

    DNA immunization was discovered in early 1990s and its use has been expanded from vaccine studies to a broader range of biomedical research, such as the generation of high quality polyclonal and monoclonal antibodies as research reagents. In this unit, three common DNA immunization methods are described: needle injection, electroporation and gene gun. In addition, several common considerations related to DNA immunization are discussed.

  8. DNA deoxyribophosphodiesterase.

    OpenAIRE

    Franklin, W A; Lindahl, T

    1988-01-01

    A previously unrecognized enzyme acting on damaged termini in DNA is present in Escherichia coli. The enzyme catalyses the hydrolytic release of 2-deoxyribose-5-phosphate from single-strand interruptions in DNA with a base-free residue on the 5' side. The partly purified protein appears to be free from endonuclease activity for apurinic/apyrimidinic sites, exonuclease activity and DNA 5'-phosphatase activity. The enzyme has a mol. wt of approximately 50,000-55,000 and has been termed DNA deox...

  9. DNA nanobiostructures

    OpenAIRE

    Rashid Bashir

    2001-01-01

    Recent advances in the field of nanotechnology and nanobiotechnology have been fuelled by the advancement in fabrication technologies that allow construction of artificial structures that are the same size or smaller than many biological entities.

  10. [Advances in Molecular Cloning].

    Science.gov (United States)

    Ashwini, M; Murugan, S B; Balamurugan, S; Sathishkumar, R

    2016-01-01

    "Molecular cloning" meaning creation of recombinant DNA molecules has impelled advancement throughout life sciences. DNA manipulation has become easy due to powerful tools showing exponential growth in applications and sophistication of recombinant DNA technology. Cloning genes has become simple what led to an explosion in the understanding of gene function by seamlessly stitching together multiple DNA fragments or by the use of swappable gene cassettes, maximizing swiftness and litheness. A novel archetype might materialize in the near future with synthetic biology techniques that will facilitate quicker assembly and iteration of DNA clones, accelerating the progress of gene therapy vectors, recombinant protein production processes and new vaccines by in vitro chemical synthesis of any in silico-specified DNA construct. The advent of innovative cloning techniques has opened the door to more refined applications such as identification and mapping of epigenetic modifications and high-throughput assembly of combinatorial libraries. In this review, we will examine the major breakthroughs in cloning techniques and their applications in various areas of biological research that have evolved mainly due to easy construction of novel expression systems. PMID:27028806

  11. Effects of Concurrent Chemoradiotherapy for EB Virus DNA Levels in Plasma of Patients with Advanced Nasopharyngeal Carcinoma%同期放化疗对晚期鼻咽癌患者血浆 EB 病毒 DNA 水平的影响

    Institute of Scientific and Technical Information of China (English)

    矫德馨; 龚智强; 贾鑑慧

    2015-01-01

    目的:探讨同期放化疗对晚期鼻咽癌患者血浆EB病毒DNA水平的影响。方法选取98例晚期鼻咽癌患者作为研究对象,采用放疗联合紫杉醇化疗进行治疗,并对98例患者血浆EBV-DNA 水平采用荧光定量PCR 技术进行测定,并与其影像学检查及病理结果进行比较分析。结果放化疗后鼻咽癌患者52例缓解,21例稳定,25例进展。三组鼻咽癌患者血浆EB-DNA水平测定阳性率缓解组为0、稳定组为4.76%,进展组最高为88.00%,缓解组与稳定组比较,差异无统计学意义(P>0.05),进展组分别与缓解组、稳定组比较,差异均具有统计学意义(P<0.05);3组敏感性分别为0、4.76%、88.00%,特异性分别为100.00%、95.24%、12.00%,阴性预测值分别为69.33%、26.67%、4.00%,阳性预测值分别为0、4.35%、95.65%;缓解组特异性和阴性预测值最高,与进展组比较,差异有统计学意义( P<0.05);进展组敏感性和阳性预测值最高,与缓解组和稳定组比较,差异有统计学意义(P<0.05)。结论晚期鼻咽癌患者同期放化疗后血浆EB病毒DNA水平,可作为监测和反映鼻咽癌患者放化疗后转移、复发的重要指标。%Objective To investigate the effect of concurrent chemoradiotherapy for EB virus DNA levels in plasma of patients with advanced nasopharyngeal carcinoma .Methods 98 patients with advanced nasopharyngeal carcinoma received radia-tion therapy combined with paclitaxel chemotherapy , and plasma EBV-DNA level of 98 patients were measured by quantitative PCR and was compared with imaging and pathology results .Results After chemoradiotherapy ,there were 52 cases of remission , 21 cases of stable and 25 cases of progress.Positive rate of plasma EB-DNA level in remission group was 0,stable group was 4.76%,progressive group was 88.00%,the difference was not statistically significant

  12. Advances in DNA methylation: 5-hydroxymethylcytosine revisited

    DEFF Research Database (Denmark)

    Dahl, Christina; Grønbæk, Kirsten; Guldberg, Per

    high levels in the brain, and TET1 has been shown to be important for self-renewal and maintenance of embryonic stem cells. Future challenges include better understanding the normal molecular, cellular and physiological roles of 5hmC and TET proteins, understanding the exact roles of TET proteins in...... modification involved in gene regulation, X-chromosome inactivation, genomic imprinting, long-term silencing of transposons and cancer development is well described. 5hmC, on the other hand, has only recently entered center stage when it was shown that the Ten-Eleven-Translocation (TET) family of oxygenases...... cancer development, and developing sequencing methodologies that can accurately distinguish among cytosine, 5mC and 5hmC at single-base-pair resolution....

  13. Cleaving DNA with DNA

    OpenAIRE

    Carmi, Nir; Balkhi, Shameelah R.; Breaker, Ronald R.

    1998-01-01

    A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This “deoxyribozyme” can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a kobs of 0.2 min−1, whereas the corresponding uncatalyzed reaction could not be detected. The duplex and triplex recognition domai...

  14. DNA nanotechnology-enabled biosensors.

    Science.gov (United States)

    Chao, Jie; Zhu, Dan; Zhang, Yinan; Wang, Lianhui; Fan, Chunhai

    2016-02-15

    Biosensors employ biological molecules to recognize the target and utilize output elements which can translate the biorecognition event into electrical, optical or mass-sensitive signals to determine the quantities of the target. DNA-based biosensors, as a sub-field to biosensor, utilize DNA strands with short oligonucleotides as probes for target recognition. Although DNA-based biosensors have offered a promising alternative for fast, simple and cheap detection of target molecules, there still exist key challenges including poor stability and reproducibility that hinder their competition with the current gold standard for DNA assays. By exploiting the self-recognition properties of DNA molecules, researchers have dedicated to make versatile DNA nanostructures in a highly rigid, controllable and functionalized manner, which offers unprecedented opportunities for developing DNA-based biosensors. In this review, we will briefly introduce the recent advances on design and fabrication of static and dynamic DNA nanostructures, and summarize their applications for fabrication and functionalization of DNA-based biosensors. PMID:26212206

  15. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.;

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  16. The Balancing Act of Ribonucleotides in DNA.

    Science.gov (United States)

    Cerritelli, Susana M; Crouch, Robert J

    2016-05-01

    The abundance of ribonucleotides in DNA remained undetected until recently because they are efficiently removed by the ribonucleotide excision repair (RER) pathway, a process similar to Okazaki fragment (OF) processing after incision by Ribonuclease H2 (RNase H2). All DNA polymerases incorporate ribonucleotides during DNA synthesis. How many, when, and why they are incorporated has been the focus of intense work during recent years by many labs. In this review, we discuss recent advances in ribonucleotide incorporation by eukaryotic DNA polymerases that suggest an evolutionarily conserved role for ribonucleotides in DNA. We also review the data that indicate that removal of ribonucleotides has an important role in maintaining genome stability. PMID:26996833

  17. Advanced Environmental Monitoring Technologies

    Science.gov (United States)

    Jan, Darrell

    2004-01-01

    Viewgraphs on Advanced Environmental Monitoring Technologies are presented. The topics include: 1) Monitoring & Controlling the Environment; 2) Illustrative Example: Canary 3) Ground-based Commercial Technology; 4) High Capability & Low Mass/Power + Autonomy = Key to Future SpaceFlight; 5) Current Practice: in Flight; 6) Current Practice: Post Flight; 7) Miniature Mass Spectrometer for Planetary Exploration and Long Duration Human Flight; 8) Hardware and Data Acquisition System; 9) 16S rDNA Phylogenetic Tree; and 10) Preview of Porter.

  18. Role of DNA profiling in forensic odontology.

    Science.gov (United States)

    Sakari, S Leena; Jimson, Sudha; Masthan, K M K; Jacobina, Jenita

    2015-04-01

    The recent advances in DNA profiling have made DNA evidence to be more widely accepted in courts. This has revolutionized the aspect of forensic odontology. DNA profiling/DNA fingerprinting has come a long way from the conventional fingerprints. DNA that is responsible for all the cell's activities, yields valuable information both in the healthy and diseased individuals. When other means of traditional identification become impossible following mass calamities or fire explosions, teeth provide a rich source of DNA as they have a high chemical as well as physical resistance. The recent evolution in the isolation of DNA and the ways of running a DNA fingerprint are highlighted in this literature review. PMID:26015692

  19. Role of DNA profiling in forensic odontology

    Directory of Open Access Journals (Sweden)

    S Leena Sakari

    2015-01-01

    Full Text Available The recent advances in DNA profiling have made DNA evidence to be more widely accepted in courts. This has revolutionized the aspect of forensic odontology. DNA profiling/DNA fingerprinting has come a long way from the conventional fingerprints. DNA that is responsible for all the cell′s activities, yields valuable information both in the healthy and diseased individuals. When other means of traditional identification become impossible following mass calamities or fire explosions, teeth provide a rich source of DNA as they have a high chemical as well as physical resistance. The recent evolution in the isolation of DNA and the ways of running a DNA fingerprint are highlighted in this literature review.

  20. Role of DNA profiling in forensic odontology

    Science.gov (United States)

    Sakari, S. Leena; Jimson, Sudha; Masthan, K. M. K.; Jacobina, Jenita

    2015-01-01

    The recent advances in DNA profiling have made DNA evidence to be more widely accepted in courts. This has revolutionized the aspect of forensic odontology. DNA profiling/DNA fingerprinting has come a long way from the conventional fingerprints. DNA that is responsible for all the cell's activities, yields valuable information both in the healthy and diseased individuals. When other means of traditional identification become impossible following mass calamities or fire explosions, teeth provide a rich source of DNA as they have a high chemical as well as physical resistance. The recent evolution in the isolation of DNA and the ways of running a DNA fingerprint are highlighted in this literature review. PMID:26015692

  1. DNA probes

    International Nuclear Information System (INIS)

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  2. [DNA computing].

    Science.gov (United States)

    Błasiak, Janusz; Krasiński, Tadeusz; Popławski, Tomasz; Sakowski, Sebastian

    2011-01-01

    Biocomputers can be an alternative for traditional "silicon-based" computers, which continuous development may be limited due to further miniaturization (imposed by the Heisenberg Uncertainty Principle) and increasing the amount of information between the central processing unit and the main memory (von Neuman bottleneck). The idea of DNA computing came true for the first time in 1994, when Adleman solved the Hamiltonian Path Problem using short DNA oligomers and DNA ligase. In the early 2000s a series of biocomputer models was presented with a seminal work of Shapiro and his colleguas who presented molecular 2 state finite automaton, in which the restriction enzyme, FokI, constituted hardware and short DNA oligomers were software as well as input/output signals. DNA molecules provided also energy for this machine. DNA computing can be exploited in many applications, from study on the gene expression pattern to diagnosis and therapy of cancer. The idea of DNA computing is still in progress in research both in vitro and in vivo and at least promising results of these research allow to have a hope for a breakthrough in the computer science. PMID:21735816

  3. Triplex technology in studies of DNA damage, DNA repair, and mutagenesis.

    Science.gov (United States)

    Mukherjee, Anirban; Vasquez, Karen M

    2011-08-01

    Triplex-forming oligonucleotides (TFOs) can bind to the major groove of homopurine-homopyrimidine stretches of double-stranded DNA in a sequence-specific manner through Hoogsteen hydrogen bonding to form DNA triplexes. TFOs by themselves or conjugated to reactive molecules can be used to direct sequence-specific DNA damage, which in turn results in the induction of several DNA metabolic activities. Triplex technology is highly utilized as a tool to study gene regulation, molecular mechanisms of DNA repair, recombination, and mutagenesis. In addition, TFO targeting of specific genes has been exploited in the development of therapeutic strategies to modulate DNA structure and function. In this review, we discuss advances made in studies of DNA damage, DNA repair, recombination, and mutagenesis by using triplex technology to target specific DNA sequences. PMID:21501652

  4. DNA Modifications by Novel Antitumor Platinum Drugs

    Czech Academy of Sciences Publication Activity Database

    Brabec, Viktor

    Kiev : National Taras Shevchenko University, 2001, s. SC-L3. [NATO Advanced Research Workshop Autumn School: Frontiers in Molecular-Scale Science and Technology of Fullerene, Nanotube, Nanosilicon and Biopolymer (DNA, Protein) Multifunctional Nanosystems. Kiev (UA), 09.09.2001-12.09.2001] Institutional research plan: CEZ:AV0Z5004920 Keywords : DNA * antitumor * platinum drugs Subject RIV: BO - Biophysics

  5. Replication licensing and the DNA damage checkpoint

    OpenAIRE

    Cook, Jeanette Gowen

    2009-01-01

    Accurate and timely duplication of chromosomal DNA requires that replication be coordinated with processes that ensure genome integrity. Significant advances in determining how the earliest steps in DNA replication are affected by DNA damage have highlighted some of the mechanisms to establish that coordination. Recent insights have expanded the relationship between the ATM and ATR-dependent checkpoint pathways and the proteins that bind and function at replication origins. These findings sug...

  6. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  7. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  8. Ancient DNA

    OpenAIRE

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of t...

  9. DNA Photolyasen

    OpenAIRE

    Maul, Melanie

    2009-01-01

    Neben der fehlerfreien Weitergabe der genetischen Information während der Zellteilung durch einen intakten Replikationsapparat, ist auch die Aufrechterhaltung der genetischen Integrität der DNA durch Reparaturenzyme entscheidend für das Überleben der Zellen, sowie für einen gesunden Organismus. Um die genomische Integrität zu wahren, entwickelten sich im Laufe der Evolution verschiedene Mechanismen, u.a. die Exzisionreparatur von geschädigter DNA oder die direkte chemische R...

  10. DNA damage

    OpenAIRE

    Kumari, Sunita; Rastogi, Rajesh P.; Singh, Kanchan L.; Singh, Shailendra P; Sinha, Rajeshwar P.

    2008-01-01

    Even under the best of circumstances, DNA is constantly subjected to chemical modifications. Several types of DNA damage such as SSB (single strand break), DSB (double strand break), CPDs (cyclobutane pyrimidine dimers), 6-4PPs (6-4 photoproducts) and their Dewar valence isomers have been identified that result from alkylating agents, hydrolytic deamination, free radicals and reactive oxygen species formed by various photochemical processes including UV radiation. There are a n...

  11. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  12. The advances in the study of circulating DNA in early diagnosis and treatment for hepatocellular carcinoma%外周血循环DNA在肝细胞癌早期诊治的研究进展

    Institute of Scientific and Technical Information of China (English)

    胡捷; 周俭; 王征; 樊嘉

    2009-01-01

    Circulating DNA is cell-free DNA existing in plasma or serum. It has already been verified that circulating DNA of cancer patients is derived from tumor cells. Therefore, it is of great value to detect the changes in the quantity and quality of the circulating DNA in cancer patients for early diagnosis and prognosis. The advantages of the detection of circulating DNA such as micro-trauma, convenient access to samples, possibility of continuous and dynamic monitoring, make it a promising tumor mark. This review recapitulates the application of circulating DNA analysis in hepatocellular carcinoma patients for diagnosis and prognosis.%循环DNA是存在于血浆/血清中的游离DNA.已有研究证实肿瘤患者循环DNA来源于肿瘤细胞.因此,检测肿瘤患者循环DNA质和量的改变对肿瘤的早期诊断和预后分析具有较大价值.循环DNA检测具有微创性、标本获取方便、可连续动态检测等优点,是一种极具前景的肿瘤标志物.有关肝癌患者循环DNA的研究不多,本文就循环DNA检测在肝癌诊断和预后分析中的研究进展做一综述.

  13. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  14. Advanced Ceramics

    International Nuclear Information System (INIS)

    The First Florida-Brazil Seminar on Materials and the Second State Meeting about new materials in Rio de Janeiro State show the specific technical contribution in advanced ceramic sector. The others main topics discussed for the development of the country are the advanced ceramic programs the market, the national technic-scientific capacitation, the advanced ceramic patents, etc. (C.G.C.)

  15. DNA nanotechnology

    Directory of Open Access Journals (Sweden)

    Nadrian C Seeman

    2003-01-01

    We are all aware that the DNA found in cells is a double helix consisting of two antiparallel strands held together by specific hydrogen-bonded base pairs; adenine (A always pairs with thymine (T, and guanine (G always pairs with cytosine (C. The specificity of this base pairing and the ability to ensure that it occurs in this fashion (and not some other1 is key to the use of DNA in materials applications. The double helical arrangement of the two molecules leads to a linear helix axis, linear not in the geometrical sense of being a straight line, but in the topological sense of being unbranched. Genetic engineers discovered in the 1970s how to splice together pieces of DNA to add new genes to DNA molecules2, and synthetic chemists worked out convenient syntheses for short pieces of DNA (up to ∼100–150 units in the 1980s3. Regardless of the impact of these technologies on biological systems, hooking together linear molecules leads only to longer linear molecules, with circles, knots, and catenanes perhaps resulting from time to time.

  16. Food Fish Identification from DNA Extraction through Sequence Analysis

    Science.gov (United States)

    Hallen-Adams, Heather E.

    2015-01-01

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

  17. Non-invasive detection of genomic imbalances in Hodgkin/Reed-Sternberg cells in early and advanced stage Hodgkin's lymphoma by sequencing of circulating cell-free DNA: a technical proof-of-principle study

    OpenAIRE

    Vandenberghe, Peter; Wlodarska, Iwona; Tousseyn, Thomas; Dehaspe, Luc; Dierickx, Daan; Verheecke, Magali; Uyttebroeck, Anne; Bechter, Oliver; Delforge, Michel; Vandecaveye, Vincent; Brison, Nathalie; Verhoef, Gregor; Legius, Eric; Amant, Frédéric; Vermeesch, Joris

    2015-01-01

    Hodgkin's lymphoma is one of the most common lymphoid neoplasms in young adults, but the low abundance of neoplastic Hodgkin/Reed-Sternberg cells in the tumour hampers the elucidation of its pathogenesis, biology, and diversity. After an incidental observation that genomic aberrations known to occur in Hodgkin's lymphoma were detectable in circulating cell-free DNA, this study was undertaken to investigate whether circulating cell-free DNA can be informative about genomic imbalances in Hodgki...

  18. DNA nanotechnology

    OpenAIRE

    Seeman, Nadrian C.

    2003-01-01

    Since Watson and Crick’s determination of its structure nearly 50 years ago, DNA has come to fill our lives in many areas, from genetic counseling to forensics, from genomics to gene therapy. These, and other ways in which DNA affects human activities, are related to its function as genetic material, not just our genetic material, but the genetic material of all living organisms. Here, we will ignore DNA’s biological role; rather, we will discuss how the properties that make it so successful ...

  19. DNA损伤修复机制和糖尿病造成的动脉粥样硬化%Advances in the Relationship between DNA Damage Repair Mechanism and Diabetic Atherosclerosis

    Institute of Scientific and Technical Information of China (English)

    曾理(综述); 丁群芳(审校)

    2015-01-01

    Atherosclerosis and the subsequent cardiovascular complications such as myocardial infarc-tion,stroke,and coronary atherosclerotic heart disease are major causes of death among the elderly. DNA damage is the cause of the activation of the DNA damage repair pathway resulting in cell senescence,and the evidence that DNA damage and DNA damage repair mechanism participate in the process of atherosclerosis has been found in some studies. Diabetes,as a risk factor of cardiovascular disease,can lead to DNA damage, so as to accelerate the aging of blood vessels. Here is to make a review of the research development of DNA damage and DNA double strand damage repair mechanism,to provide a new method to prevent and treat ath-erosclerosis.%动脉粥样硬化及其所引起的心肌梗死、脑卒中、冠状动脉粥样硬化性心脏病(冠心病)等是导致老年人病死率增加的重要原因。 DNA损伤是激活DNA损伤修复路径导致细胞早衰的重要原因,而动脉粥样硬化中存在DNA损伤及DNA损伤修复机制参与的证据。糖尿病作为心血管疾病危险因素具有导致DNA损伤,从而加速血管老化的作用。该文综述了动脉粥样硬化疾病中DNA损伤和DNA双链损伤修复机制的研究进展,从而为防治动脉粥样硬化疾病提供新的思路。

  20. Wireframe and tensegrity DNA nanostructures.

    Science.gov (United States)

    Simmel, Stephanie S; Nickels, Philipp C; Liedl, Tim

    2014-06-17

    nanotechnology starting with the construction of four-way junctions and then allude to simple geometric objects such as the wireframe cube presented by Nadrian Seeman along with a variety of triangulated wireframe constructions. We examine DNA tensegrity triangles that self-assemble into crystals with sizes of several hundred micrometers as well as prestressed DNA origami tensegrity architecture, which uses single-stranded DNA with its entropic spring behavior as tension bearing components to organize stiff multihelix bundles in three dimensions. Finally, we discuss emerging applications of the aforementioned design principles in diverse fields such as diagnostics, drug delivery, or crystallography. Despite great advances in related research fields like protein and RNA engineering, DNA self-assembly is currently the most accessible technique to organize matter on the nanoscale, and we expect many more exciting applications to emerge. PMID:24720250

  1. Synthetic DNA

    OpenAIRE

    O’ Driscoll, Aisling; Sleator, Roy D.

    2013-01-01

    With world wide data predicted to exceed 40 trillion gigabytes by 2020, big data storage is a very real and escalating problem. Herein, we discuss the utility of synthetic DNA as a robust and eco-friendly archival data storage solution of the future.

  2. DNA Investigations.

    Science.gov (United States)

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  3. DNA repair in cancer: emerging targets for personalized therapy

    International Nuclear Information System (INIS)

    Genomic deoxyribonucleic acid (DNA) is under constant threat from endogenous and exogenous DNA damaging agents. Mammalian cells have evolved highly conserved DNA repair machinery to process DNA damage and maintain genomic integrity. Impaired DNA repair is a major driver for carcinogenesis and could promote aggressive cancer biology. Interestingly, in established tumors, DNA repair activity is required to counteract oxidative DNA damage that is prevalent in the tumor microenvironment. Emerging clinical data provide compelling evidence that overexpression of DNA repair factors may have prognostic and predictive significance in patients. More recently, DNA repair inhibition has emerged as a promising target for anticancer therapy. Synthetic lethality exploits intergene relationships where the loss of function of either of two related genes is nonlethal, but loss of both causes cell death. Exploiting this approach by targeting DNA repair has emerged as a promising strategy for personalized cancer therapy. In the current review, we focus on recent advances with a particular focus on synthetic lethality targeting in cancer

  4. Advances of DNA Damage Repair and Cisplatin Resistance Mechanisms in Lung Cancer%DNA损伤修复与肺癌顺铂耐药机制的研究进展

    Institute of Scientific and Technical Information of China (English)

    唐春兰

    2011-01-01

    Lung cancer is the most common cause of death from cancer worldwide per year. Platinum-based combination chemotherapy is a main treatment of lung cancer. Cisplatin is adopted widely and used effectively in the first-line chemotherapy. Unfortunately, development of cisplatin resistance is a major obstacle to the success of lung caner. Cisplatin is a cell-cycle-non-specific cytotoxic drugs and its main target is DNA. Thus, defective DNA damage repair is one of the main mechanisms of cisplatin resistance. In this review, we will focus on the defective DNA damage repair in cisplatin resistance of lung cancer including nucleotide excision repair, DNA mismatch repair, DNA double-strand break repair and translesion synthesis.%肺癌是目前世界上致死率最高的恶性肿瘤,化疗是治疗的主要手段之一,肺癌的化疗是以铂类为基础的联合化疗,其中,顺铂是有效并广泛应用的一线药物,但是由于耐药问题的存在使其疗效不尽如人意.顺铂是一种细胞周期非特异性细胞毒药物,其主要作用靶点是DNA,因此DNA损伤修复功能的异常是顺铂耐药的主要机制之一.本文主要综述了与肺癌顺铂耐药相关的DNA损伤修复异常,包括核苷酸切除修复异常、碱基错配修复异常、DNA双链断裂损伤修复异常及跨损伤修复.

  5. Advances of Total DNA Extraction Technology for Soil Microbial Diversity Research%土壤微生物多样性研究中总DNA提取技术进展

    Institute of Scientific and Technical Information of China (English)

    肖斌; 蒋代华; 刘立龙; 刘全东

    2012-01-01

    The influencing factors and application aspects, as well as the potentials and limitations of DNA extraction techniques for microbial diversity analysis were reviewed. Applying appropriate methods to extract microorganism DNA fragment that have right purity and appropriate size from soil were the precondition in soil microbial study on the molecular level, and the subsequent molecular biotechnology operations were all rely on these methods.%综述了在土壤微生物多样性研究中总DNA提取技术的研究进展,分析了DNA提取过程中的主要影响因素及存在的问题.

  6. DNA Methylation

    OpenAIRE

    İzmirli, Müzeyyen; Tufan, Turan; Alptekin, Davut

    2012-01-01

    Methylation is a chemical reaction in biological systems for normal genome regulation and development. It is a well known type of epigenetic mechanism. Methylation which regulates gene expression via epigenetic events like gene activation, repression, and chromatin remodelling, consists of two methylation systems. One of these systems is DNA methylation whereas the other is protein (histone) methylation. These systems are associated with some fundamental abnormalities and diseases. This revi...

  7. DNA Nanorobotics

    OpenAIRE

    Hamdi M; Ferreira A

    2006-01-01

    This paper presents a molecular mechanics study for new nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics simulation the behavior of bionanorobotic components and structures through 3-D visualization. The main novelty of the proposed simulations is based on the mechanical characterization of passive/active robotic devices based on double stranded DNA molecules. Their ...

  8. DNA Methylation

    OpenAIRE

    Muzeyyen Izmirli; Turan Tufan; Davut Alptekin

    2012-01-01

    Methylation is a chemical reaction in biological systems for normal genome regulation and development. It is a well known type of epigenetic mechanism. Methylation which regulates gene expression via epigenetic events like gene activation, repression, and chromatin remodelling, consists of two methylation systems. One of these systems is DNA methylation whereas the other is protein (histone) methylation. These systems are associated with some fundamental abnormalities and diseases. This revie...

  9. Mendel Meets CSI: Forensic Genotyping as a Method to Teach Genetics & DNA Science

    Science.gov (United States)

    Kurowski, Scotia; Reiss, Rebecca

    2007-01-01

    This article describes a forensic DNA science laboratory exercise for advanced high school and introductory college level biology courses. Students use a commercial genotyping kit and genetic analyzer or gene sequencer to analyze DNA recovered from a fictitious crime scene. DNA profiling and STR genotyping are outlined. DNA extraction, PCR, and…

  10. ADVANCE PAYMENTS

    CERN Multimedia

    Human Resources Division

    2002-01-01

    Administrative Circular Nº 8 makes provision for the granting of advance payments, repayable in several monthly instalments, by the Organization to the members of its personnel. Members of the personnel are reminded that these advances are only authorized in exceptional circumstances and at the discretion of the Director-General. In view of the current financial situation of the Organization, and in particular the loans it will have to incur, the Directorate has decided to restrict the granting of such advances to exceptional or unforeseen circumstances entailing heavy expenditure and more specifically those pertaining to social issues. Human Resources Division Tel. 73962

  11. Advance payments

    CERN Multimedia

    Human Resources Division

    2003-01-01

    Administrative Circular N 8 makes provision for the granting of advance payments, repayable in several monthly instalments, by the Organization to the members of its personnel. Members of the personnel are reminded that these advances are only authorized in exceptional circumstances and at the discretion of the Director-General. In view of the current financial situation of the Organization, and in particular the loans it will have to incur, the Directorate has decided to restrict the granting of such advances to exceptional or unforeseen circumstances entailing heavy expenditure and more specifically those pertaining to social issues. Human Resources Division Tel. 73962

  12. Distinct DNA methylomes of newborns and centenarians

    Science.gov (United States)

    Heyn, Holger; Li, Ning; Ferreira, Humberto J.; Moran, Sebastian; Pisano, David G.; Gomez, Antonio; Diez, Javier; Sanchez-Mut, Jose V.; Setien, Fernando; Carmona, F. Javier; Puca, Annibale A.; Sayols, Sergi; Pujana, Miguel A.; Serra-Musach, Jordi; Iglesias-Platas, Isabel; Formiga, Francesc; Fernandez, Agustin F.; Fraga, Mario F.; Heath, Simon C.; Valencia, Alfonso; Gut, Ivo G.; Wang, Jun; Esteller, Manel

    2012-01-01

    Human aging cannot be fully understood in terms of the constrained genetic setting. Epigenetic drift is an alternative means of explaining age-associated alterations. To address this issue, we performed whole-genome bisulfite sequencing (WGBS) of newborn and centenarian genomes. The centenarian DNA had a lower DNA methylation content and a reduced correlation in the methylation status of neighboring cytosine—phosphate—guanine (CpGs) throughout the genome in comparison with the more homogeneously methylated newborn DNA. The more hypomethylated CpGs observed in the centenarian DNA compared with the neonate covered all genomic compartments, such as promoters, exonic, intronic, and intergenic regions. For regulatory regions, the most hypomethylated sequences in the centenarian DNA were present mainly at CpG-poor promoters and in tissue-specific genes, whereas a greater level of DNA methylation was observed in CpG island promoters. We extended the study to a larger cohort of newborn and nonagenarian samples using a 450,000 CpG-site DNA methylation microarray that reinforced the observation of more hypomethylated DNA sequences in the advanced age group. WGBS and 450,000 analyses of middle-age individuals demonstrated DNA methylomes in the crossroad between the newborn and the nonagenarian/centenarian groups. Our study constitutes a unique DNA methylation analysis of the extreme points of human life at a single-nucleotide resolution level. PMID:22689993

  13. Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma.

    Science.gov (United States)

    Burnham, Philip; Kim, Min Seong; Agbor-Enoh, Sean; Luikart, Helen; Valantine, Hannah A; Khush, Kiran K; De Vlaminck, Iwijn

    2016-01-01

    Circulating cell-free DNA (cfDNA) is emerging as a powerful monitoring tool in cancer, pregnancy and organ transplantation. Nucleosomal DNA, the predominant form of plasma cfDNA, can be adapted for sequencing via ligation of double-stranded DNA (dsDNA) adapters. dsDNA library preparations, however, are insensitive to ultrashort, degraded cfDNA. Drawing inspiration from advances in paleogenomics, we have applied a single-stranded DNA (ssDNA) library preparation method to sequencing of cfDNA in the plasma of lung transplant recipients (40 samples, six patients). We found that ssDNA library preparation yields a greater portion of sub-100 bp nuclear genomic cfDNA (p 10(-5), Mann-Whitney U Test), and an increased relative abundance of mitochondrial (10.7x, p 10(-5)) and microbial cfDNA (71.3x, p 10(-5)). The higher yield of microbial sequences from this method increases the sensitivity of cfDNA-based monitoring for infections following transplantation. We detail the fragmentation pattern of mitochondrial, nuclear genomic and microbial cfDNA over a broad fragment length range. We report the observation of donor-specific mitochondrial cfDNA in the circulation of lung transplant recipients. A ssDNA library preparation method provides a more informative window into understudied forms of cfDNA, including mitochondrial and microbial derived cfDNA and short nuclear genomic cfDNA, while retaining information provided by standard dsDNA library preparation methods. PMID:27297799

  14. Advanced Microsensors

    Science.gov (United States)

    1991-01-01

    This video looks at a spinoff application of the technology from advanced microsensors -- those that monitor and determine conditions of spacecraft like the Space Shuttle. The application featured is concerned with the monitoring of the health of premature babies.

  15. Advanced nanoelectronics

    CERN Document Server

    Ismail, Razali

    2012-01-01

    While theories based on classical physics have been very successful in helping experimentalists design microelectronic devices, new approaches based on quantum mechanics are required to accurately model nanoscale transistors and to predict their characteristics even before they are fabricated. Advanced Nanoelectronics provides research information on advanced nanoelectronics concepts, with a focus on modeling and simulation. Featuring contributions by researchers actively engaged in nanoelectronics research, it develops and applies analytical formulations to investigate nanoscale devices. The

  16. DNA repair

    International Nuclear Information System (INIS)

    In this chapter a series of DNA repair pathways are discussed which are available to the cell to cope with the problem of DNA damaged by chemical or physical agents. In the case of microorganisms our knowledge about the precise mechanism of each DNA repair pathway and the regulation of it has been improved considerably when mutants deficient in these repair mechanisms became available. In the case of mammalian cells in culture, until recently there were very little repair deficient mutants available, because in almost all mammalian cells in culture at least the diploid number of chromosomes is present. Therefore the frequency of repair deficient mutants in such populations is very low. Nevertheless because replica plating techniques are improving some mutants from Chinese hamsters ovary cells and L5178Y mouse lymphoma cells are now available. In the case of human cells, cultures obtained from patients with certain genetic diseases are available. A number of cells appear to be sensitive to some chemical or physical mutagens. These include cells from patients suffering from xeroderma pigmentosum, Ataxia telangiectasia, Fanconi's anemia, Cockayne's syndrome. However, only in the case of xeroderma pigmentosum cells, has the sensitivity to ultraviolet light been clearly correlated with a deficiency in excision repair of pyrimidine dimers. Furthermore the work with strains obtained from biopsies from man is difficult because these cells generally have low cloning efficiencies and also have a limited lifespan in vitro. It is therefore very important that more repair deficient mutants will become available from established cell lines from human or animal origin

  17. Forensic DNA methylation profiling from evidence material for investigative leads.

    Science.gov (United States)

    Lee, Hwan Young; Lee, Soong Deok; Shin, Kyoung-Jin

    2016-07-01

    DNA methylation is emerging as an attractive marker providing investigative leads to solve crimes in forensic genetics. The identification of body fluids that utilizes tissue-specific DNA methylation can contribute to solving crimes by predicting activity related to the evidence material. The age estimation based on DNA methylation is expected to reduce the number of potential suspects, when the DNA profile from the evidence does not match with any known person, including those stored in the forensic database. Moreover, the variation in DNA implicates environmental exposure, such as cigarette smoking and alcohol consumption, thereby suggesting the possibility to be used as a marker for predicting the lifestyle of potential suspect. In this review, we describe recent advances in our understanding of DNA methylation variations and the utility of DNA methylation as a forensic marker for advanced investigative leads from evidence materials. [BMB Reports 2016; 49(7): 359-369]. PMID:27099236

  18. Wrinkled DNA.

    OpenAIRE

    Arnott, S.; Chandrasekaran, R.; Puigjaner, L C; Walker, J K; Hall, I H; Birdsall, D L; Ratliff, R L

    1983-01-01

    The B form of poly d(GC):poly d(GC) in orthorhombic microcrystallites in oriented fibers has a secondary structure in which a dinucleotide is the repeated motif rather than a mononucleotide as in standard, smooth B DNA. One set of nucleotides (probably GpC) has the same conformations as the smooth form but the alternate (CpG) nucleotides have a different conformation at C3'-O3'. This leads to a distinctive change in the orientation of the phosphate groups. Similar perturbations can be detecte...

  19. Active DNA Demethylation Mediated by DNA Glycosylases

    OpenAIRE

    Zhu, Jian-Kang

    2009-01-01

    Active DNA demethylation is involved in many vital developmental and physiological processes of plants and animals. Recent genetic and biochemical studies in Arabidopsis have demonstrated that a subfamily of DNA glycosylases function to promote DNA demethylation through a base excision-repair pathway. These specialized bifunctional DNA glycosylases remove the 5-methylcytosine base and then cleave the DNA backbone at the abasic site, resulting in a gap that is then filled with an unmethylated ...

  20. AdvancED Flex 4

    CERN Document Server

    Tiwari, Shashank; Schulze, Charlie

    2010-01-01

    AdvancED Flex 4 makes advanced Flex 4 concepts and techniques easy. Ajax, RIA, Web 2.0, mashups, mobile applications, the most sophisticated web tools, and the coolest interactive web applications are all covered with practical, visually oriented recipes. * Completely updated for the new tools in Flex 4* Demonstrates how to use Flex 4 to create robust and scalable enterprise-grade Rich Internet Applications.* Teaches you to build high-performance web applications with interactivity that really engages your users.* What you'll learn Practiced beginners and intermediate users of Flex, especially

  1. φ29 DNA polymerase

    OpenAIRE

    Blanco, Luis; Bernad, Antonio; Salas, Margarita

    1996-01-01

    An improved method for determining the nucleotide base sequence of a DNA molecule employs a φ-29 type DNA polymerase modified to have reduced or no exonuclease activity. The method includes annealing the DNA molecule with a primer molecule able to hybridize to the DNA molecule; incubating the annealed mixture in a vessel containing four different deoxynucleoside triphosphates, a DNA polymerase, and one or more DNA synthesis terminating agents which terminate DNA synthesis at a specific nucleo...

  2. Tumorigenic DNA viruses

    Energy Technology Data Exchange (ETDEWEB)

    Klein, G.

    1989-01-01

    The eighth volume of Advances in Viral Oncology focuses on the three major DNA virus groups with a postulated or proven tumorigenic potential: papillomaviruses, animal hepatitis viruses, and the Epstein-Bar virus. In the opening chapters, the contributors analyze the evidence that papillomaviruses and animal hepatitis viruses are involved in tumorigenesis and describe the mechanisms that trigger virus-host cell interactions. A detailed section on the Epstein-Barr virus (EBV) - comprising more than half the book - examines the transcription and mRNA processing patterns of the virus genome; the mechanisms by which EBV infects lymphoid and epithelial cells; the immunological aspects of the virus; the actions of EBV in hosts with Acquired Immune Deficiency Syndrome; and the involvement of EBV in the etiology of Burkitt's lymphoma.

  3. DNA detection using recombination proteins.

    Directory of Open Access Journals (Sweden)

    Olaf Piepenburg

    2006-07-01

    Full Text Available DNA amplification is essential to most nucleic acid testing strategies, but established techniques require sophisticated equipment or complex experimental procedures, and their uptake outside specialised laboratories has been limited. Our novel approach, recombinase polymerase amplification (RPA, couples isothermal recombinase-driven primer targeting of template material with strand-displacement DNA synthesis. It achieves exponential amplification with no need for pretreatment of sample DNA. Reactions are sensitive, specific, and rapid and operate at constant low temperature. We have also developed a probe-based detection system. Key aspects of the combined RPA amplification/detection process are illustrated by a test for the pathogen methicillin-resistant Staphylococcus aureus. The technology proves to be sensitive to fewer than ten copies of genomic DNA. Furthermore, products can be detected in a simple sandwich assay, thereby establishing an instrument-free DNA testing system. This unique combination of properties is a significant advance in the development of portable and widely accessible nucleic acid-based tests.

  4. DNA ligase I, the replicative DNA ligase

    OpenAIRE

    Howes, Timothy R.L.; Tomkinson, Alan E.

    2012-01-01

    Multiple DNA ligation events are required to join the Okazaki fragments generated during lagging strand DNA synthesis. In eukaryotes, this is primarily carried out by members of the DNA ligase I family. The C-terminal catalytic region of these enzymes is composed of three domains: a DNA binding domain, an adenylation domain and an OB-fold domain. In the absence of DNA, these domains adopt an extended structure but transition into a compact ring structure when they engage a DNA nick, with each...

  5. Sequence Affects the Cyclization of DNA Minicircles.

    Science.gov (United States)

    Wang, Qian; Pettitt, B Montgomery

    2016-03-17

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

  6. Trabectedin – the DNA minor groove binder

    Directory of Open Access Journals (Sweden)

    G. A. Belitsky

    2015-01-01

    Full Text Available Trabectedin (ET-743, Yondelis is an alkaloid that was originally isolated from the Caribbean Sea squirt, Ecteinascidia turbinata and is now produced synthetically. Its chemical structure consists in three fused tetrahydroisoquinoline rings. Two of them, A and B, binds covalently to guanine residues in the minor groove of the DNA double helix to bend the molecule toward the major groove and the third ring C protrudes from the DNA duplex, apparently allowing interactions with several nuclear proteins. Binding to the minor groove of DNA, trabectedin trigger a cascade of events that interfere with several transcription factors, DNA binding proteins, and DNA repair pathways in particular nucleotide excision repair. It acts both as a DNA-alkylating drug and topoisomerase poison. Trabectedin-DNA adduct traps the nucleotide excision repair proteins repairing the DNA damage in transcribing genes and induces DNA strand breaks. Cells deficient in homologous recombination pathway which repairs these double-strand breaks show increased sensitivity to trabectedin. The most sensitive of them were myxoid liposarcomas. Trabectedin is also effective in chemotherapy-experienced patients with advanced, recurrent liposarcoma or leiomyosarcoma as well as in women with ovarian cancer and breast cancer with BRCAness phenotype. Besides of tumor cells Trabectedin inhibits inflammatory cells by affecting directly monocytes and tumorassociated macrophages and indirectly by inhibiting production of inflammatory mediators, the cytokines and chemokines. It inhibits also the MDR-1 gene, which is responsible for the resistance of cancer cells to chemotherapeutic agents and strikes tumor angiogenesis.

  7. j5 DNA assembly design automation software.

    Science.gov (United States)

    Hillson, Nathan J; Rosengarten, Rafael D; Keasling, Jay D

    2012-01-20

    Recent advances in Synthetic Biology have yielded standardized and automatable DNA assembly protocols that enable a broad range of biotechnological research and development. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. Here, we report the development and deployment of a web-based software tool, j5, which automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. Using a GFP expression testbed, we demonstrate that j5 designs can be executed with the SLIC, Gibson, or CPEC assembly methods, used to build combinatorial libraries with the Golden Gate assembly method, and applied to the preparation of linear gene deletion cassettes for E. coli. The DNA assembly design algorithms reported here are generally applicable to broad classes of DNA construction methodologies and could be implemented to supplement other DNA assembly design tools. Taken together, these innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design. PMID:23651006

  8. Advanced calculus

    CERN Document Server

    Nickerson, HK; Steenrod, NE

    2011-01-01

    ""This book is a radical departure from all previous concepts of advanced calculus,"" declared the Bulletin of the American Mathematics Society, ""and the nature of this departure merits serious study of the book by everyone interested in undergraduate education in mathematics."" Classroom-tested in a Princeton University honors course, it offers students a unified introduction to advanced calculus. Starting with an abstract treatment of vector spaces and linear transforms, the authors introduce a single basic derivative in an invariant form. All other derivatives - gradient, divergent, curl,

  9. Recent advances of protein microarrays

    OpenAIRE

    Hultschig, Claus; Kreutzberger, Jürgen; Seitz, Harald; Konthur, Zoltán; Büssow, Konrad; Lehrach, Hans

    2006-01-01

    Technological innovations and novel applications have greatly advanced the field of protein microarrays. Over the past two years, different types of protein microarrays have been used for serum profiling, protein abundance determinations, and identification of proteins that bind DNA or small compounds. However, considerable development is still required to ensure common quality standards and to establish large content repertoires. Here, we summarize applications available to date and discuss ...

  10. Advanced ferroelectricity

    CERN Document Server

    Blinc, R

    2011-01-01

    Advances in the field of ferroelectricity have implications both for basic physics and for technological applications such as memory devices, spintronic applications and electro-optic devices, as well as in acoustics, robotics, telecommunications and medicine. This book provides an account of recent developments in the field.

  11. ATRF Houses the Latest DNA Sequencing Technologies | Poster

    Science.gov (United States)

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

  12. The polymer physics of single DNA confined in nanochannels.

    Science.gov (United States)

    Dai, Liang; Renner, C Benjamin; Doyle, Patrick S

    2016-06-01

    In recent years, applications and experimental studies of DNA in nanochannels have stimulated the investigation of the polymer physics of DNA in confinement. Recent advances in the physics of confined polymers, using DNA as a model polymer, have moved beyond the classic Odijk theory for the strong confinement, and the classic blob theory for the weak confinement. In this review, we present the current understanding of the behaviors of confined polymers while briefly reviewing classic theories. Three aspects of confined DNA are presented: static, dynamic, and topological properties. The relevant simulation methods are also summarized. In addition, comparisons of confined DNA with DNA under tension and DNA in semidilute solution are made to emphasize universal behaviors. Finally, an outlook of the possible future research for confined DNA is given. PMID:26782150

  13. DNA modifications: Another stable base in DNA

    Science.gov (United States)

    Brazauskas, Pijus; Kriaucionis, Skirmantas

    2014-12-01

    Oxidation of 5-methylcytosine has been proposed to mediate active and passive DNA demethylation. Tracking the history of DNA modifications has now provided the first solid evidence that 5-hydroxymethylcytosine is a stable epigenetic modification.

  14. The initiation mechanism of translesion DNA synthesis in response to UV irradiation

    International Nuclear Information System (INIS)

    Ultraviolet (UV) light causes DNA damage and increases a person's risk for both melanoma and non-melanoma skin cancer. If the DNA damage is unrepaired, cells can often tolerate it by using specialized DNA polymerases during DNA replication to insert a base opposite a lesion and bypass the damage, in a process called translesion DNA synthesis (TLS). This review addresses recent advances in our understanding of TLS. (author)

  15. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  16. Sperm DNA oxidative damage and DNA adducts.

    Science.gov (United States)

    Jeng, Hueiwang Anna; Pan, Chih-Hong; Chao, Mu-Rong; Lin, Wen-Yi

    2015-12-01

    The objective of this study was to investigate DNA damage and adducts in sperm from coke oven workers who have been exposed to polycyclic aromatic hydrocarbons. A longitudinal study was conducted with repeated measurements during spermatogenesis. Coke-oven workers (n=112) from a coke-oven plant served the PAH-exposed group, while administrators and security personnel (n=67) served the control. Routine semen parameters (concentration, motility, vitality, and morphology) were analyzed simultaneously; the assessment of sperm DNA integrity endpoints included DNA fragmentation, bulky DNA adducts, and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dGuo). The degree of sperm DNA fragmentation was measured using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay and sperm chromatin structure assay (SCSA). The PAH-exposed group had a significant increase in bulky DNA adducts and 8-oxo-dGuo compared to the control subjects (Ps=0.002 and 0.045, respectively). Coke oven workers' percentages of DNA fragmentation and denaturation from the PAH-exposed group were not significantly different from those of the control subjects (Ps=0.232 and 0.245, respectively). Routine semen parameters and DNA integrity endpoints were not correlated. Concentrations of 8-oxo-dGuo were positively correlated with percentages of DNA fragmentation measured by both TUNEL and SCSA (Ps=0.045 and 0.034, respectively). However, the concentrations of 8-oxo-dGuo and percentages of DNA fragmentation did not correlate with concentrations of bulky DNA adducts. In summary, coke oven workers with chronic exposure to PAHs experienced decreased sperm DNA integrity. Oxidative stress could contribute to the degree of DNA fragmentation. Bulky DNA adducts may be independent of the formation of DNA fragmentation and oxidative adducts in sperm. Monitoring sperm DNA integrity is recommended as a part of the process of assessing the impact of occupational and environmental toxins on sperm

  17. DNA glycosylases: in DNA repair and beyond

    OpenAIRE

    Jacobs, Angelika L.; Schär, Primo

    2011-01-01

    The base excision repair machinery protects DNA in cells from the damaging effects of oxidation, alkylation, and deamination; it is specialized to fix single-base damage in the form of small chemical modifications. Base modifications can be mutagenic and/or cytotoxic, depending on how they interfere with the template function of the DNA during replication and transcription. DNA glycosylases play a key role in the elimination of such DNA lesions; they recognize and excise damaged bases, thereb...

  18. DNA vaccines and bacterial DNA in immunity

    OpenAIRE

    Bandholtz, Lisa Charlotta

    2002-01-01

    This thesis describes DNA-based vaccination and the importance of bacterial DNA in different immunological perspectives. Intranasal (i.n.) DNA vaccination utilizing a plasmid encoding the chlamydial heat shock protein 60 (p-hsp-60) generated lower bacterial burden and reduced pathology in the lungs of mice after subsequent infection with C. pneumoniae. This DNA vaccine- induced protection was dependent on T cells and induction of IFN-gamma. Co-administration of a plasmid...

  19. 云杉属树种天然群体DNA标记的国外研究进展%Advances in Foreign Researches on DNA Markers in Spruce Natural Groups

    Institute of Scientific and Technical Information of China (English)

    罗建勋; 董昕; 辜云杰

    2012-01-01

    本文综述了自21世纪初以来DNA标记技术在国外云杉属树种中的应用情况,涉及到的树种以挪威云杉为主,多至十几种,标记种类主要包括AFLP、RAPD、RFLP、SSR、ISSR、STS、EST、VNTR和SNPs等。另外,对几种群体遗传参数进行比较分析,表明云杉天然群体遗传变异丰富,其中利用ISSR检测到白云杉天然群体多态位点百分率可达90%,利用RAPD检测到挪威云杉群体总遗传变异高至0.941;群体间存在遗传分化,产生了适应环境的变异,除一个利用mtVNTR研究所得结果外,其他研究均表明,云杉群体间遗传分化程度并不是很高,云杉群体变异主要表现为群体内变异。同时,对DNA标记在云杉属种质资源保存及遗传改良方面的前景进行了展望。%This paper deals with the application of DNA markers in spruce during the first 10 years of 21st Century.The species of spruce referred to more than 10 species,in which Norway Spruce was main.The DNA markers included AFLP,RAPD,RFLP,SSR,ISSR,STS,EST,VNTR and SNPs,etc.Moreover,several group genetic parameters were compared and analyzed.The results have shown that the genetic variation of spruce natural groups is rich.Polymorphic loci percentage of white spruce is up to 90% by ISSR.Total genetic diversity is up to 0.941 in Norway spruce detected by RAPD.The genetic differentiation between groups displays that a new variation fit for environment changing has occurred.All the results except one with mtVNTR indicate that the level of genetic differentiation among groups is low and main variation lies in inter-group.Meanwhile,this review also forecasts the application of DNA markers in the field of germ plasm resource conservation and genetic improvement.

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

    International Nuclear Information System (INIS)

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

  1. DNA encoding a DNA repair protein

    Science.gov (United States)

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-08-15

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  2. Dental DNA fingerprinting in identification of human remains

    OpenAIRE

    K L Girish; Farzan S Rahman; Tippu, Shoaib R

    2010-01-01

    The recent advances in molecular biology have revolutionized all aspects of dentistry. DNA, the language of life yields information beyond our imagination, both in health or disease. DNA fingerprinting is a tool used to unravel all the mysteries associated with the oral cavity and its manifestations during diseased conditions. It is being increasingly used in analyzing various scenarios related to forensic science. The technical advances in molecular biology have propelled the analysis of the...

  3. DNA Microarray-Based Diagnostics.

    Science.gov (United States)

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

    2016-01-01

    The DNA microarray technology is currently a useful biomedical tool which has been developed for a variety of diagnostic applications. However, the development pathway has not been smooth and the technology has faced some challenges. The reliability of the microarray data and also the clinical utility of the results in the early days were criticized. These criticisms added to the severe competition from other techniques, such as next-generation sequencing (NGS), impacting the growth of microarray-based tests in the molecular diagnostic market.Thanks to the advances in the underlying technologies as well as the tremendous effort offered by the research community and commercial vendors, these challenges have mostly been addressed. Nowadays, the microarray platform has achieved sufficient standardization and method validation as well as efficient probe printing, liquid handling and signal visualization. Integration of various steps of the microarray assay into a harmonized and miniaturized handheld lab-on-a-chip (LOC) device has been a goal for the microarray community. In this respect, notable progress has been achieved in coupling the DNA microarray with the liquid manipulation microsystem as well as the supporting subsystem that will generate the stand-alone LOC device.In this chapter, we discuss the major challenges that microarray technology has faced in its almost two decades of development and also describe the solutions to overcome the challenges. In addition, we review the advancements of the technology, especially the progress toward developing the LOC devices for DNA diagnostic applications. PMID:26614075

  4. Biotechnological advances in Lilium.

    Science.gov (United States)

    Bakhshaie, Mehdi; Khosravi, Solmaz; Azadi, Pejman; Bagheri, Hedayat; van Tuyl, Jaap M

    2016-09-01

    Modern powerful techniques in plant biotechnology have been developed in lilies (Lilium spp., Liliaceae) to propagate, improve and make new phenotypes. Reliable in vitro culture methods are available to multiply lilies rapidly and shorten breeding programs. Lilium is also an ideal model plant to study in vitro pollination and embryo rescue methods. Although lilies are recalcitrant to genetic manipulation, superior genotypes are developed with improved flower colour and form, disease resistance and year round forcing ability. Different DNA molecular markers have been developed for rapid indirect selection, genetic diversity evaluation, mutation detection and construction of Lilium linkage map. Some disease resistance-QTLs are already mapped on the Lilium linkage map. This review presents latest information on in vitro propagation, genetic engineering and molecular advances made in lily. PMID:27318470

  5. Advanced Virgo

    CERN Multimedia

    Virgo, a first-generation interferometric gravitational wave (GW) detector, located in the European Gravitational Observatory, EGO, Cascina (Pisa-Italy) and constructed by the collaboration of French and Italian institutes (CNRS and INFN) has successfully completed its long-duration data taking runs. It is now undergoing a fundamental upgrade that exploits available cutting edges technology to open an exciting new window on the universe, with the first detection of a gravitational wave signal. Advanced Virgo (AdV) is the project to upgrade the Virgo detector to a second-generation instrument. AdV will be able to scan a volume of the Universe 1000 times larger than initial Virgo. AdV will be hosted in the same infrastructures as Virgo. The Advanced VIRGO project is funded and at present carried on by a larger collaboration of institutes belonging to CNRS- France , RMKI - Hungary, INFN- Italy, Nikhef - The Netherlands Polish Academy of Science - Poland.

  6. Activation and Regulation of DNA-Driven Immune Responses

    OpenAIRE

    Paludan, Søren R

    2015-01-01

    The innate immune system provides early defense against infections and also plays a key role in monitoring alterations of homeostasis in the body. DNA is highly immunostimulatory, and recent advances in this field have led to the identification of the innate immune sensors responsible for the recognition of DNA as well as the downstream pathways that are activated. Moreover, information on how cells regulate DNA-driven immune responses to avoid excessive inflammation is now emerging. Finally,...

  7. Streamlined Purification of Plasmid DNA From Prokaryotic Cultures

    OpenAIRE

    Pueschel, Laura; Li, Hongshan; Hymes, Matthew

    2011-01-01

    We describe the complete process of AcroPrep Advance Filter Plates for 96 plasmid preparations, starting from prokaryotic culture and ending with high purity DNA. Based on multi-well filtration for bacterial lysate clearance and DNA purification, this method creates a streamlined process for plasmid preparation. Filter plates containing silica-based media can easily be processed by vacuum filtration or centrifuge to yield appreciable quantities of plasmid DNA. Quantitative analyses determine ...

  8. Interpreting DNA mixtures with relatives of a missing suspect

    OpenAIRE

    Hu, YQ; Fung, WK; Choy, YT

    2011-01-01

    Recent advances in DNA profiling have been proven extremely useful for forensic human identification. DNA mixtures are commonly found in serious crimes such as rape as well as voluminous crimes like theft. In this paper, one general formula is obtained for the evaluation of DNA mixtures when the suspect is unavailable for typing, but one maternal and one paternal relatives of the suspect are typed instead. In principle, closer relatives of the suspect will provide more genetic information on ...

  9. Advanced Nanoemulsions

    Science.gov (United States)

    Fryd, Michael M.; Mason, Thomas G.

    2012-05-01

    Recent advances in the growing field of nanoemulsions are opening up new applications in many areas such as pharmaceuticals, foods, and cosmetics. Moreover, highly controlled nanoemulsions can also serve as excellent model systems for investigating basic scientific questions about soft matter. Here, we highlight some of the most recent developments in nanoemulsions, focusing on methods of formation, surface modification, material properties, and characterization. These developments provide insight into the substantial advantages that nanoemulsions can offer over their microscale emulsion counterparts.

  10. Advanced LIGO

    OpenAIRE

    Aasi, J.; Abbott, B.; Abbott, R.; Abbott, T.; Abernathy, M; Ackley, K.; Adams, C.; Adams, T.; Addesso, P.; Adhikari, R.; Adya, V.; Affeldt, C.; Aggarwal, N.; Aguiar, O.; Ain, A.

    2014-01-01

    The Advanced LIGO gravitational wave detectors are second-generation instruments designed and built for the two LIGO observatories in Hanford, WA and Livingston, LA, USA. The two instruments are identical in design, and are specialized versions of a Michelson interferometer with 4 km long arms. As in Initial LIGO, Fabry–Perot cavities are used in the arms to increase the interaction time with a gravitational wave, and power recycling is used to increase the effective laser power. Signal recyc...

  11. Advanced Combustion

    Energy Technology Data Exchange (ETDEWEB)

    Holcomb, Gordon R. [NETL

    2013-03-11

    The activity reported in this presentation is to provide the mechanical and physical property information needed to allow rational design, development and/or choice of alloys, manufacturing approaches, and environmental exposure and component life models to enable oxy-fuel combustion boilers to operate at Ultra-Supercritical (up to 650{degrees}C & between 22-30 MPa) and/or Advanced Ultra-Supercritical conditions (760{degrees}C & 35 MPa).

  12. Dynamics and control of DNA sequence amplification

    International Nuclear Information System (INIS)

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

  13. Dynamics and control of DNA sequence amplification

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-28

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

  14. Temperature Dependent Kinetics DNA Charge Transport

    Science.gov (United States)

    Wohlgamuth, Chris; McWilliams, Marc; Slinker, Jason

    2012-10-01

    Charge transport (CT) through DNA has been extensively studied, and yet the mechanism of this process is still not yet fully understood. Besides the benefits of understanding charge transport through this fundamental molecule, further understanding of this process will elucidate the biological implications of DNA CT and advance sensing technology. Therefore, we have investigated the temperature dependence of DNA CT by measuring the electrochemistry of DNA monolayers modified with a redox-active probe. By using multiplexed electrodes on silicon chips, we compare square wave voltammetry of distinct DNA sequences under identical experimental conditions. We vary the probe length within the well matched DNA duplex in order to investigate distance dependent kinetics. This length dependent study is a necessary step to understanding the dominant mechanism behind DNA CT. Using a model put forth by O'Dea and Osteryoung and applying a nonlinear least squares analysis we are able to determine the charge transfer rates (k), transfer coefficients (α), and the total surface concentration (&*circ;) of the DNA monolayer. Arrhenius like behavior is observed for the multiple probe locations, and the results are viewed in light of and compared to the prominent charge transport mechanisms.

  15. Azidophenyl as a click-transformable redox label of DNA suitable for electrochemical detection of DNA-protein interactions

    Czech Academy of Sciences Publication Activity Database

    Balintová, Jana; Brázdová, Marie; Fojta, Miroslav; Hocek, Michal

    Praha : Czech Chemical Society, 2014. s. 32. [Liblice 2014. Advances in Organic, Bioorganic and Pharmaceutical Chemistry /49./. 07.11.2014-09.11.2014, Lázně Bělohrad] R&D Projects: GA ČR GBP206/12/G151 Institutional support: RVO:61388963 ; RVO:68081707 Keywords : DNA * redox labeling * DNA-protein interactions Subject RIV: CC - Organic Chemistry

  16. Human placental DNA methyltransferase: DNA substrate and DNA binding specificity.

    OpenAIRE

    Wang, R.Y.; Huang, L. H.; Ehrlich, M

    1984-01-01

    We have partially purified a DNA methyltransferase from human placenta using a novel substrate for a highly sensitive assay of methylation of hemimethylated DNA. This substrate was prepared by extensive nick translation of bacteriophage XP12 DNA, which normally has virtually all of its cytosine residues replaced by 5-methylcytosine (m5C). Micrococcus luteus DNA was just as good a substrate if it was first similarly nick translated with m5dCTP instead of dCTP in the polymerization mixture. At ...

  17. Structural Insight into the DNA-Binding Mode of the Primosomal Proteins PriA, PriB, and DnaT

    Directory of Open Access Journals (Sweden)

    Yen-Hua Huang

    2014-01-01

    Full Text Available Replication restart primosome is a complex dynamic system that is essential for bacterial survival. This system uses various proteins to reinitiate chromosomal DNA replication to maintain genetic integrity after DNA damage. The replication restart primosome in Escherichia coli is composed of PriA helicase, PriB, PriC, DnaT, DnaC, DnaB helicase, and DnaG primase. The assembly of the protein complexes within the forked DNA responsible for reloading the replicative DnaB helicase anywhere on the chromosome for genome duplication requires the coordination of transient biomolecular interactions. Over the last decade, investigations on the structure and mechanism of these nucleoproteins have provided considerable insight into primosome assembly. In this review, we summarize and discuss our current knowledge and recent advances on the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT.

  18. Advanced DVI+

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Tae Soon; Lee, S. T.; Euh, D. J.; Chu, I. C.; Youn, Y. J. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2012-10-15

    A new advanced safety feature of DVI+ (Direct Vessel Injection Plus) for the APR+ (Advanced Power Reactor Plus), to mitigate the ECC (Emergency Core Cooling) bypass fraction and to prevent switching an ECC outlet to a break flow inlet during a DVI line break, is presented for an advanced DVI system. In the current DVI system, the ECC water injected into the downcomer is easily shifted to the broken cold leg by a high steam cross flow which comes from the intact cold legs during the late reflood phase of a LBLOCA (Large Break Loss Of Coolant Accident). For the new DVI+ system, an ECBD (Emergency Core Barrel Duct) is installed on the outside of a core barrel cylinder. The ECBD has a gap (From the core barrel wall to the ECBD inner wall to the radial direction) of 3/25-7/25 of the downcomer annulus gap. The DVI nozzle and the ECBD are only connected by the ECC water jet, which is called a hydrodynamic water bridge, during the ECC injection period. Otherwise these two components are disconnected from each other without any pipes inside the downcomer. The ECBD is an ECC downward isolation flow sub-channel which protects the ECC water from the high speed steam crossflow in the downcomer annulus during a LOCA event. The injected ECC water flows downward into the lower downcomer through the ECBD without a strong entrainment to a steam cross flow. The outer downcomer annulus of the ECBD is the major steam flow zone coming from the intact cold leg during a LBLOCA. During a DVI line break, the separated DVI nozzle and ECBD have the effect of preventing the level of the cooling water from being lowered in the downcomer due to an inlet-outlet reverse phenomenon at the lowest position of the outlet of the ECBD.

  19. Advanced mathematics

    CERN Document Server

    Gupta, CB; Kumar, V

    2009-01-01

    About the Book: This book `Advanced Mathematics` is primarily designed for B.Tech., IV Semester (EE and EC branch) students of Rajasthan Technical University. The subject matter is discussed in a lucid manner. The discussion is covered in five units: Unit I: deals with Numerical Analysis, Unit-II: gives different aspects of Numerical Analysis, Unit-III: Special Function, Unit-IV:Statistics and Probability, Calculus of Variation and Transforms are discussed in Unit V. All the theoretical concepts are explained through solved examples. Besides, a large number of unsolved problems on each top

  20. Advanced calculus

    CERN Document Server

    Friedman, Avner

    2007-01-01

    This rigorous two-part treatment advances from functions of one variable to those of several variables. Intended for students who have already completed a one-year course in elementary calculus, it defers the introduction of functions of several variables for as long as possible, and adds clarity and simplicity by avoiding a mixture of heuristic and rigorous arguments.The first part explores functions of one variable, including numbers and sequences, continuous functions, differentiable functions, integration, and sequences and series of functions. The second part examines functions of several

  1. DNA extraction by zinc.

    OpenAIRE

    Kejnovský, E; Kypr, J

    1997-01-01

    A fast, very simple and efficient method of DNA extraction is described which takes advantage of DNA sedimentation induced by millimolar concentrations of ZnCl2. The zinc-induced sedimentation is furthermore strongly promoted by submillimolar phosphate anion concentrations. Within 90% of DNA irrespective of whether a plasmid DNA or short oligonucleotides are the extracted material. The method works with plasmid DNA and oligonucleotide concentrations as low as 100 ng/ml and 10 microg/ml, respe...

  2. Wedging out DNA damage

    OpenAIRE

    Schärer, Orlando D.; Campbell, Arthur J

    2009-01-01

    The DNA-repair machinery is faced with the significant challenge of differentiating DNA lesions from unmodified DNA. Two recent publications, one in this issue of Nature Structural & Molecular Biology, uncover a new way of recognizing minimally distorting DNA lesions: insertion of a 3- or 4-amino-acid wedge into DNA to extrude the lesion into a shallow binding pocket that can accommodate various damaged bases.

  3. Getting Ready for the Dance: FANCJ Irons Out DNA Wrinkles.

    Science.gov (United States)

    Bharti, Sanjay Kumar; Awate, Sanket; Banerjee, Taraswi; Brosh, Robert M

    2016-01-01

    Mounting evidence indicates that alternate DNA structures, which deviate from normal double helical DNA, form in vivo and influence cellular processes such as replication and transcription. However, our understanding of how the cellular machinery deals with unusual DNA structures such as G-quadruplexes (G4), triplexes, or hairpins is only beginning to emerge. New advances in the field implicate a direct role of the Fanconi Anemia Group J (FANCJ) helicase, which is linked to a hereditary chromosomal instability disorder and important for cancer suppression, in replication past unusual DNA obstacles. This work sets the stage for significant progress in dissecting the molecular mechanisms whereby replication perturbation by abnormal DNA structures leads to genomic instability. In this review, we focus on FANCJ and its role to enable efficient DNA replication when the fork encounters vastly abundant naturally occurring DNA obstacles, which may have implications for targeting rapidly dividing cancer cells. PMID:27376332

  4. Advanced LIGO

    CERN Document Server

    ,

    2014-01-01

    The Advanced LIGO gravitational wave detectors are second generation instruments designed and built for the two LIGO observatories in Hanford, WA and Livingston, LA. The two instruments are identical in design, and are specialized versions of a Michelson interferometer with 4 km long arms. As in initial LIGO, Fabry-Perot cavities are used in the arms to increase the interaction time with a gravitational wave, and power recycling is used to increase the effective laser power. Signal recycling has been added in Advanced LIGO to improve the frequency response. In the most sensitive frequency region around 100 Hz, the design strain sensitivity is a factor of 10 better than initial LIGO. In addition, the low frequency end of the sensitivity band is moved from 40 Hz down to 10 Hz. All interferometer components have been replaced with improved technologies to achieve this sensitivity gain. Much better seismic isolation and test mass suspensions are responsible for the gains at lower frequencies. Higher laser power, ...

  5. 3DNA: A Tool for DNA Sculpting

    OpenAIRE

    Gupta, Shikhar Kumar; Joshi, Foram; Limbachiya, Dixita; Gupta, Manish K.

    2014-01-01

    DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures. One such technique involves the implementation of DNA Bricks proposed by Ke et al., 2012 to create complex three-dimensional (3D) structures. Modeling these DNA nano structures can prove to be a cumbersome and tedious task. Exploiting the programmability of b...

  6. DNA Polymerase-Catalyzed DNA Network Growth

    OpenAIRE

    Keller, Sascha; Wang, Jie; Chandra, Madhaviah; Berger, Rüdiger; Marx, Andreas

    2008-01-01

    The distinct base pairing property of DNA is an advantageous phenomenon that has been exploited in the usage of DNA as scaffold for directed self-organization to form nanometer-sized objects in a desirable fashion. Herein we report the construction of three-dimensional DNA-based networks that can be generated and amplified by the DNA polymerase chain reaction (PCR). The approach is flexible allowing tuning of the meshes of the network by variation of the size of the template. Additionally, fu...

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

    Science.gov (United States)

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

    2016-01-01

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

  8. DNA polymerase δ and DNA repair: DNA repair synthesis in human fibroblasts requires DNA polymerase δ

    International Nuclear Information System (INIS)

    When UV-irradiated cultured diploid human fibroblasts were permeabilized with Brij-58 then separated from soluble material by centrifugation, conservative DNA repair synthesis could be restored by a soluble factor obtained from the supernate of similarly treated HeLa cells. Monoclonal antibody to KB cell DNA polymerase α, while binding to HeLa DNA polymerase α, did not bind to the HeLa DNA polymerase δ. Moreover, at micromolar concentrations N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate (BuPdGT) and 2(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate (BuAdATP) were potent inhibitors of DNA polymerase α, but did not inhibit the DNA polymerase δ. Neither purified DNA polymerase α nor β could promote repair DNA synthesis in the permeabilized cells. Furthermore, if monoclonal antibodies to DNA polymerase α BuPdGTP, or BuAdATP was added to the reconstituted system, there was no significant inhibition

  9. DNA-nanostructure-assembly by sequential spotting

    Directory of Open Access Journals (Sweden)

    Breitenstein Michael

    2011-11-01

    Full Text Available Abstract Background The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions. Results For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid to incorporate advanced structures. Conclusions The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element.

  10. Dental DNA fingerprinting in identification of human remains

    Directory of Open Access Journals (Sweden)

    K L Girish

    2010-01-01

    Full Text Available The recent advances in molecular biology have revolutionized all aspects of dentistry. DNA, the language of life yields information beyond our imagination, both in health or disease. DNA fingerprinting is a tool used to unravel all the mysteries associated with the oral cavity and its manifestations during diseased conditions. It is being increasingly used in analyzing various scenarios related to forensic science. The technical advances in molecular biology have propelled the analysis of the DNA into routine usage in crime laboratories for rapid and early diagnosis. DNA is an excellent means for identification of unidentified human remains. As dental pulp is surrounded by dentin and enamel, which forms dental armor, it offers the best source of DNA for reliable genetic type in forensic science. This paper summarizes the recent literature on use of this technique in identification of unidentified human remains.

  11. DNA fragmentation in apoptosis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    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. DNA damage and autophagy

    International Nuclear Information System (INIS)

    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.

  13. DNA Open states and DNA hydratation

    International Nuclear Information System (INIS)

    It is a very well-known fact that an protonic exchange exists among natural DNA filaments and synthetic polynucleotides with the solvent (1--2). The existence of DNA open states, that is to say states for which the interior of the DNA molecule is exposed to the external environment, it has been demonstrated by means of proton-deuterium exchange (3). This work has carried out experiments measuring the dispersion of the traverse relaxation rate (4), as a pulsation rate function in a Carr-Purcell-Meiboom-Gill (CPMG) pulses sequence rate, to determine changes in the moist layer of the DNA molecule. The experiments were carried out under different experimental conditions in order to vary the probability that open states occurs, such as temperature or the exposure to electromagnetic fields. Some theoretical models were supposed to adjust the experimental results including those related to DNA non linear dynamic

  14. HPV DNA test

    Science.gov (United States)

    The HPV DNA test is used to check for high-risk HPV infection in women. HPV infection around the genitals is ... warts spread when you have sex. The HPV-DNA test is generally not recommended for detecting low- ...

  15. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  16. Charge transfer and transport in DNA

    OpenAIRE

    Jortner, Joshua; Bixon, Mordechai; Langenbacher, Thomas; Michel-Beyerle, Maria E.

    1998-01-01

    We explore charge migration in DNA, advancing two distinct mechanisms of charge separation in a donor (d)–bridge ({Bj})–acceptor (a) system, where {Bj} = B1,B2, … , BN are the N-specific adjacent bases of B-DNA: (i) two-center unistep superexchange induced charge transfer, d*{Bj}a → d∓{Bj}a±, and (ii) multistep charge transport involves charge injection from d* (or d+) to {Bj}, charge hopping within {Bj}, and charge trapping by a. For off-resonance coupling, mechanism i prevails with the char...

  17. Future advances.

    Science.gov (United States)

    Celesia, Gastone G; Hickok, Gregory

    2015-01-01

    Future advances in the auditory systems are difficult to predict, and only educated guesses are possible. It is expected that innovative technologies in the field of neuroscience will be applied to the auditory system. Optogenetics, Brainbow, and CLARITY will improve our knowledge of the working of neural auditory networks and the relationship between sound and language, providing a dynamic picture of the brain in action. CLARITY makes brain tissue transparent and offers a three-dimensional view of neural networks, which, combined with genetically labeling neurons with multiple, distinct colors (Optogenetics), will provide detailed information of the complex brain system. Molecular functional magnetic resonance imaging (MRI) will allow the study of neurotransmitters detectable by MRI and their function in the auditory pathways. The Human Connectome project will study the patterns of distributed brain activity that underlie virtually all aspects of cognition and behavior and determine if abnormalities in the distributed patterns of activity may result in hearing and behavior disorders. Similarly, the programs of Big Brain and ENIGMA will improve our understanding of auditory disorders. New stem-cell therapy and gene therapies therapy may bring about a partial restoration of hearing for impaired patients by inducing regeneration of cochlear hair cells. PMID:25726297

  18. Recombinant DNA in Medicine

    OpenAIRE

    Cederbaum, Stephen D.; Fareed, George C.; Lovett, Michael A.; Shapiro, Larry J.

    1984-01-01

    Studies in bacteria and bacterial viruses have led to methods to manipulate and recombine DNA in unique and reproducible ways and to amplify these recombined molecules millions of times. Once properly identified, the recombinant DNA molecules can be used in various ways useful in medicine and human biology. There are many applications for recombinant DNA technology. Cloned complementary DNA has been used to produce various human proteins in microorganisms. Insulin and growth hormone have been...

  19. Is DNA a language?

    Science.gov (United States)

    Tsonis, A A; Elsner, J B; Tsonis, P A

    1997-01-01

    DNA sequences usually involve local construction rules that affect different scales. As such their "dictionary" may not follow Zipf's law (a power law) which is followed in every natural language. Indeed, analysis of many DNA sequences suggests that no linguistics connections to DNA exist and that even though it has structure DNA is not a language. Computer simulations and a biological approach to this problem further support these results. PMID:9039397

  20. DNA Damage Response

    OpenAIRE

    Giglia-Mari, Giuseppina; Zotter, Angelika; Vermeulen, Wim

    2011-01-01

    Structural changes to DNA severely affect its functions, such as replication and transcription, and play a major role in age-related diseases and cancer. A complicated and entangled network of DNA damage response (DDR) mechanisms, including multiple DNA repair pathways, damage tolerance processes, and cell-cycle checkpoints safeguard genomic integrity. Like transcription and replication, DDR is a chromatin-associated process that is generally tightly controlled in time and space. As DNA damag...

  1. DNA-Mediated Electrochemistry

    OpenAIRE

    Gorodetsky, Alon A.; Buzzeo, Marisa C.; Barton, Jacqueline K.

    2008-01-01

    The base pair stack of DNA has been demonstrated as a medium for long-range charge transport chemistry both in solution and at DNA-modified surfaces. This chemistry is exquisitely sensitive to structural perturbations in the base pair stack as occur with lesions, single base mismatches, and protein binding. We have exploited this sensitivity for the development of reliable electrochemical assays based on DNA charge transport at self-assembled DNA monolayers. Here, we discuss the characteristi...

  2. Transcriptional quiescence of paternal mtDNA in cyprinid fish embryos.

    Science.gov (United States)

    Wen, Ming; Peng, Liangyue; Hu, Xinjiang; Zhao, Yuling; Liu, Shaojun; Hong, Yunhan

    2016-01-01

    Mitochondrial homoplasmy signifies the existence of identical copies of mitochondrial DNA (mtDNA) and is essential for normal development, as heteroplasmy causes abnormal development and diseases in human. Homoplasmy in many organisms is ensured by maternal mtDNA inheritance through either absence of paternal mtDNA delivery or early elimination of paternal mtDNA. However, whether paternal mtDNA is transcribed has remained unknown. Here we report that paternal mtDNA shows late elimination and transcriptional quiescence in cyprinid fishes. Paternal mtDNA was present in zygotes but absent in larvae and adult organs of goldfish and blunt-snout bream, demonstrating paternal mtDNA delivery and elimination for maternal mtDNA inheritance. Surprisingly, paternal mtDNA remained detectable up to the heartbeat stage, suggesting its late elimination leading to embryonic heteroplasmy up to advanced embryogenesis. Most importantly, we never detected the cytb RNA of paternal mtDNA at all stages when paternal mtDNA was easily detectable, which reveals that paternal mtDNA is transcriptionally quiescent and thus excludes its effect on the development of heteroplasmic embryos. Therefore, paternal mtDNA in cyprinids shows late elimination and transcriptional quiescence. Clearly, transcriptional quiescence of paternal mtDNA represents a new mechanism for maternal mtDNA inheritance and provides implications for treating mitochondrion-associated diseases by mitochondrial transfer or replacement. PMID:27334806

  3. Highly Effective DNA Extraction Method from Fresh, Frozen, Dried and Clotted Blood Samples

    OpenAIRE

    Jaleh Barar; Sina Atashpaz; Abolfazl Barzegari; Vala Kafil; Sepideh Zununi Vahed; Farzaneh Soltanzad; Sara Samadi Shams

    2011-01-01

    Introduction: Today, with the tremendous potential of genomics and other recent advances in science, the role of science to improve reliable DNA extraction methods is more relevant than ever before. The ideal process for genomic DNA extraction demands high quantities of pure, integral and intact genomic DNA (gDNA) from the sample with minimal co-extraction of inhibitors of downstream processes. Here, we report the development of a very rapid, less-hazardous, and high throughput protocol for e...

  4. DNA evidence: current perspective and future challenges in India.

    Science.gov (United States)

    Verma, Sunil K; Goswami, Gajendra K

    2014-08-01

    Since the discovery of DNA fingerprinting technology in 1985 it has been used extensively as evidence in the court of law world-wide to establish the individual identity both in civil and criminal matters. In India, the first case of parentage dispute solved by the use of DNA fingerprinting technology was in 1989. Since then till date, the DNA technology has been used not only to resolve the cases of paternity and maternity disputes, but also for the establishment of individual identity in various criminal cases and for wildlife forensic identification. Since last half a decade, India is exercising to enact legislation on the use of DNA in the judicial realm and the draft 'Human DNA Bill-2012' is pending in the parliament. Largely, the promoters of forensic DNA testing have anticipated that DNA tests are nearly infallible and DNA technology could be the greatest single advance step in search for truth, conviction of the perpetrator, and acquittal of the innocent. The current article provides a comprehensive review on the status of DNA testing in India and elucidates the consequences of the admissibility of DNA as 'evidence' in the judicial dominion. In this backdrop of civil and criminal laws and changing ethical and societal attitudes, it is concluded that the DNA legislation in India and world-wide needs to be designed with utmost care. PMID:24967868

  5. A novel constraint for thermodynamically designing DNA sequences.

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

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

  6. A novel constraint for thermodynamically designing DNA sequences.

    Science.gov (United States)

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

    2013-01-01

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

  7. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  8. DNA damage response

    NARCIS (Netherlands)

    G. Giglia-Mari (Giuseppina); A. Zotter (Angelika); W. Vermeulen (Wim)

    2011-01-01

    textabstractStructural changes to DNA severely affect its functions, such as replication and transcription, and play a major role in age-related diseases and cancer. A complicated and entangled network ofDNA damage response (DDR) mechanisms, including multiple DNA repair pathways, damage tolerance p

  9. DNA-Metallodrugs Interactions Signaled by Electrochemical Biosensors: An Overview

    Directory of Open Access Journals (Sweden)

    Mauro Ravera

    2007-01-01

    Full Text Available The interaction of drugs with DNA is an important aspect in pharmacology. In recent years, many important technological advances have been made to develop new techniques to monitor biorecognition and biointeraction on solid devices. The interaction between DNA and drugs can cause chemical and conformational modifications and, thus, variation of the electrochemical properties of nucleobases. The propensity of a given compound to interact with DNA is measured as a function of the decrease of guanine oxidation signal on a DNA electrochemical biosensor. Covalent binding at N7 of guanine, electrostatic interactions, and intercalation are the events that this kind of biosensor can detect. In this context, the interaction between a panel of antitumoral Pt-, Ru-, and Ti-based metallodrugs with DNA immobilized on screen-printed electrodes has been studied. The DNA biosensors are used for semiquantitative evaluation of the analogous interaction occurring in the biological environment.

  10. DNA loops and semicatenated DNA junctions

    OpenAIRE

    Strauss François; Gaillard Claire

    2000-01-01

    Abstract Background Alternative DNA conformations are of particular interest as potential signals to mark important sites on the genome. The structural variability of CA microsatellites is particularly pronounced; these are repetitive poly(CA) · poly(TG) DNA sequences spread in all eukaryotic genomes as tracts of up to 60 base pairs long. Many in vitro studies have shown that the structure of poly(CA) · poly(TG) can vary markedly from the classical right handed DNA double helix and adopt dive...

  11. Mitochondrial Dna Replacement Versus Nuclear Dna Persistence

    OpenAIRE

    Serva, Maurizio

    2006-01-01

    In this paper we consider two populations whose generations are not overlapping and whose size is large. The number of males and females in both populations is constant. Any generation is replaced by a new one and any individual has two parents for what concerns nuclear DNA and a single one (the mother) for what concerns mtDNA. Moreover, at any generation some individuals migrate from the first population to the second. In a finite random time $T$, the mtDNA of the second population is comple...

  12. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske;

    2008-01-01

    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

  13. Electronic Transport in DNA

    OpenAIRE

    Klotsa, Daphne; Römer, Rudolf A.; Turner, Matthew S.

    2005-01-01

    We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which electrons travel. Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations on poly(dG)-poly(dC), telomeric-DNA, random-ATGC DNA and lambda-DNA. We find that random and lambda-D...

  14. DNA: Structure and function

    DEFF Research Database (Denmark)

    Sinden, Richard R.; E. Pearson, Christopher; N. Potaman, Vladimir;

    1998-01-01

    This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form for a...... long period of time before its information is accessed by the cell. Although DNA plays a critical role as an informational storage molecule, it is by no means as unexciting as a computer tape or disk drive. The structure of the DNA described by Watson and Crick in 1953 is a right handed helix of two...... individual antiparallel DNA strands. Hydrogen bonds provide specificity that allows pairing between the complementary bases (A.T and G.C) in opposite strands. Base stacking occurs near the center of the DNA helix and provides a great deal of stability to the helix (in addition to hydrogen bonding). The sugar...

  15. DNA from keratinous tissue

    DEFF Research Database (Denmark)

    Olsen, Maia E.; Bengtsson, Camilla Friis; Bertelsen, Mads Frost;

    2012-01-01

    Although good quality DNA can be recovered from the base of the calamus of freshly sampled feathers, as from other fully keratinized tissues such as nail or hair shaft, the quality and quantity of DNA in the majority of feather structures is much poorer. Little research has been performed...... to characterize the quality of this DNA is, and thus what a researcher might be able to achieve when using feathers as a source of DNA. In this review, we expand on our companion article detailing the quality of DNA in nail and hair, by synthesizing published, and new preliminary genetic data obtained from...... feathers. As with nail and hair, we demonstrate that although DNA can, in general, be recovered from all parts of the feather, the quality of such DNA varies. As such, although one can expect a priori that genetic analyses are possible on the feather, for PCR based analyses, it is extremely difficult...

  16. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander

    2015-01-01

    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

  17. DNA Hairpins: Fuel for Autonomous DNA Devices

    OpenAIRE

    Green, Simon J.; Lubrich, Daniel; Turberfield, Andrew J.

    2006-01-01

    We present a study of the hybridization of complementary DNA hairpin loops, with particular reference to their use as fuel for autonomous DNA devices. The rate of spontaneous hybridization between complementary hairpins can be reduced by increasing the neck length or decreasing the loop length. Hairpins with larger loops rapidly form long-lived kissed complexes. Hairpin loops may be opened by strand displacement using an opening strand that contains the same sequence as half of the neck and a...

  18. Novel DNA probes for sensitive DNA detection

    OpenAIRE

    Richardson, James Alistair

    2010-01-01

    The ability to detect and interrogate DNA sequences allows further understanding and diagnosis of genetic disease. The ability to perform such analysis of genetic material requires highly selective and reliable technologies. Furthermore techniques which can use simple and cheap equipment allow the use of such technologies for point of care analysis. Described in this thesis are two novel DNA probe systems designed for mutation discrimination and sequence recognition of PCR pro...

  19. Fidelity of DNA polymerases in DNA amplification.

    OpenAIRE

    Keohavong, P; Thilly, W G

    1989-01-01

    Denaturing gradient gel electrophoresis (DGGE) was used to separate and isolate the products of DNA amplification by polymerase chain reaction (PCR). The strategy permitted direct enumeration and identification of point mutations created by T4, modified T7, Klenow fragment of polymerase I, and Thermus aquaticus (Taq) DNA polymerases. Incorrectly synthesized sequences were separated from the wild type by DGGE as mutant/wild-type heteroduplexes and the heteroduplex fraction was used to calculat...

  20. DNA degradation and Apoptosis : DNA degradation

    OpenAIRE

    Torriglia, Alicia; Padron, Laura

    2005-01-01

    Apoptosis, is a form of programmed cell death essential for the development and maintenance of multicellular organisms. DNA degradation is one of the hallmarks of apoptosis. The central component of the apoptotic machinery is a proteolytic system involving caspases and non-caspases proteases. CAD, a caspase-activated DNase, is the endonuclease responsible for DNA degradation during caspase-dependent apoptosis. The relationship between non-caspase proteases and endonucleases is less clear and ...

  1. MICROENCAPSULATION: ADVANCEMENTS IN APPLICATIONS

    Directory of Open Access Journals (Sweden)

    Arsh Chanana

    2013-02-01

    Full Text Available Microcapsule is a tiny sphere including core material/internal phase or fill, coated with/surrounded by wall know as shell, coating or membrane. The usual size range of the microcapsule lies between 1 to 1000 μm. The technique is usually applied for targeted drug delivery, protection of the molecule and stability if the core material. Microencapsulation system offers potential advantages over conventional drug delivery systems and also established as unique carrier systems for many pharmaceuticals. This article contains the traditional and the recent pharmaceutical applications of microecapsules. The microcapsules are widely applied in pharmaceutical for Novel drug Delivery System (NDDS, latest formulations, Delivery of DNA Vaccines, Pro Drug Approach, Biodegradable and biocompatible material. Other then pharmaceutical microcapsules are widely used in delivery of probiotic, pesticide industry, food technology, beverages and cell immobilization etc. Although significant advances have been made in the field of microencapsulation, still many challenges need to be rectified during the appropriate selection of core materials, coating materials and process techniques.

  2. Advances in Genome Biology & Technology

    Energy Technology Data Exchange (ETDEWEB)

    Thomas J. Albert, Jon R. Armstrong, Raymond K. Auerback, W. Brad Barbazuk, et al.

    2007-12-01

    This year's meeting focused on the latest advances in new DNA sequencing technologies and the applications of genomics to disease areas in biology and biomedicine. Daytime plenary sessions highlighted cutting-edge research in areas such as complex genetic diseases, comparative genomics, medical sequencing, massively parallel DNA sequencing, and synthetic biology. Technical approaches being developed and utilized in contemporary genomics research were presented during evening concurrent sessions. Also, as in previous years, poster sessions bridged the morning and afternoon plenary sessions. In addition, for the third year in a row, the Advances in Genome Biology and Technology (AGBT) meeting was preceded by a pre-meeting workshop that aimed to provide an introductory overview for trainees and other meeting attendees. This year, speakers at the workshop focused on next-generation sequencing technologies, including their experiences, findings, and helpful advise for others contemplating using these platforms in their research. Speakers from genome centers and core sequencing facilities were featured and the workshop ended with a roundtable discussion, during which speakers fielded questions from the audience.

  3. DNA analysis for mysteries buried in history

    Directory of Open Access Journals (Sweden)

    Tanuj Kanchan

    2015-09-01

    Full Text Available Over the years DNA technology has proved to be a path breaking invention and this technological advancement in modern investigations will hopefully solve many more mysteries in the time to come. However, the developing world is lagging far behind owing to financial constraints and has resorted to relatively less reliable methods during investigations. Hopefully, developing nations too will follow suit in utilizing this technology to its potential.

  4. DNA Assembly in 3D Printed Fluidics

    OpenAIRE

    Patrick, William G.; Nielsen, Alec A. K.; Keating, Steven J.; Levy, Taylor J.; Che-Wei Wang; Jaime J Rivera; Octavio Mondragón-Palomino; Carr, Peter A.; Voigt, Christopher A.; Neri Oxman; Kong, David S.

    2015-01-01

    The process of connecting genetic parts-DNA assembly-is a foundational technology for synthetic biology. Microfluidics present an attractive solution for minimizing use of costly reagents, enabling multiplexed reactions, and automating protocols by integrating multiple protocol steps. However, microfluidics fabrication and operation can be expensive and requires expertise, limiting access to the technology. With advances in commodity digital fabrication tools, it is now possible to directly p...

  5. DNA Assembly in 3D Printed Fluidics

    OpenAIRE

    Patrick, William G.; Nielsen, Alec A.K.; Keating, Steven J.; Levy, Taylor J.; Wang, Che-Wei; Rivera, Jaime J.; Mondragón-Palomino, Octavio; Carr, Peter A.; Voigt, Christopher A; Oxman, Neri; Kong, David S.

    2015-01-01

    The process of connecting genetic parts—DNA assembly—is a foundational technology for synthetic biology. Microfluidics present an attractive solution for minimizing use of costly reagents, enabling multiplexed reactions, and automating protocols by integrating multiple protocol steps. However, microfluidics fabrication and operation can be expensive and requires expertise, limiting access to the technology. With advances in commodity digital fabrication tools, it is now possible to directly p...

  6. Lattice engineering through nanoparticle-DNA frameworks

    Science.gov (United States)

    Tian, Ye; Zhang, Yugang; Wang, Tong; Xin, Huolin L.; Li, Huilin; Gang, Oleg

    2016-06-01

    Advances in self-assembly over the past decade have demonstrated that nano- and microscale particles can be organized into a large diversity of ordered three-dimensional (3D) lattices. However, the ability to generate different desired lattice types from the same set of particles remains challenging. Here, we show that nanoparticles can be assembled into crystalline and open 3D frameworks by connecting them through designed DNA-based polyhedral frames. The geometrical shapes of the frames, combined with the DNA-assisted binding properties of their vertices, facilitate the well-defined topological connections between particles in accordance with frame geometry. With this strategy, different crystallographic lattices using the same particles can be assembled by introduction of the corresponding DNA polyhedral frames. This approach should facilitate the rational assembly of nanoscale lattices through the design of the unit cell.

  7. Epigenome Maintenance in Response to DNA Damage.

    Science.gov (United States)

    Dabin, Juliette; Fortuny, Anna; Polo, Sophie E

    2016-06-01

    Organism viability relies on the stable maintenance of specific chromatin landscapes, established during development, that shape cell functions and identities by driving distinct gene expression programs. Yet epigenome maintenance is challenged during transcription, replication, and repair of DNA damage, all of which elicit dynamic changes in chromatin organization. Here, we review recent advances that have shed light on the specialized mechanisms contributing to the restoration of epigenome structure and function after DNA damage in the mammalian cell nucleus. By drawing a parallel with epigenome maintenance during replication, we explore emerging concepts and highlight open issues in this rapidly growing field. In particular, we present our current knowledge of molecular players that support the coordinated maintenance of genome and epigenome integrity in response to DNA damage, and we highlight how nuclear organization impacts genome stability. Finally, we discuss possible functional implications of epigenome plasticity in response to genotoxic stress. PMID:27259203

  8. Antiparasitic DNA vaccines in 21st century.

    Science.gov (United States)

    Wedrychowicz, Halina

    2015-06-01

    Demands for effective vaccines to control parasitic diseases of humans and livestock have been recently exacerbated by the development of resistance of most pathogenic parasites to anti-parasitic drugs. Novel genomic and proteomic technologies have provided opportunities for the discovery and improvement of DNA vaccines which are relatively easy as well as cheap to fabricate and stable at room temperatures. However, their main limitation is rather poor immunogenicity, which makes it necessary to couple the antigens with adjuvant molecules. This paper review recent advances in the development of DNA vaccines to some pathogenic protozoa and helminths. Numerous studies were conducted over the past 14 years of 21st century, employing various administration techniques, adjuvants and new immunogenic antigens to increase efficacy of DNA vaccines. Unfortunately, the results have not been rewarding. Further research is necessary using more extensive combinations of antigens; alternate delivery systems and more efficient adjuvants based on knowledge of the immunomodulatory capacities of parasitic protozoa and helminths. PMID:26203983

  9. Pseudomonas aeruginosa phage PaP1 DNA polymerase is an A-family DNA polymerase demonstrating ssDNA and dsDNA 3'-5' exonuclease activity.

    Science.gov (United States)

    Liu, Binyan; Gu, Shiling; Liang, Nengsong; Xiong, Mei; Xue, Qizhen; Lu, Shuguang; Hu, Fuquan; Zhang, Huidong

    2016-08-01

    Most phages contain DNA polymerases, which are essential for DNA replication and propagation in infected host bacteria. However, our knowledge on phage-encoded DNA polymerases remains limited. This study investigated the function of a novel DNA polymerase of PaP1, which is the lytic phage of Pseudomonas aeruginosa. PaP1 encodes its sole DNA polymerase called Gp90 that was predicted as an A-family DNA polymerase with polymerase and 3'-5' exonuclease activities. The sequence of Gp90 is homologous but not identical to that of other A-family DNA polymerases, such as T7 DNA polymerases (Pol) and DNA Pol I. The purified Gp90 demonstrated a polymerase activity. The processivity of Gp90 in DNA replication and its efficiency in single-dNTP incorporation are similar to those of T7 Pol with processive thioredoxin (T7 Pol/trx). Gp90 can degrade ssDNA and dsDNA in 3'-5' direction at a similar rate, which is considerably lower than that of T7 Pol/trx. The optimized conditions for polymerization were a temperature of 37 °C and a buffer consisting of 40 mM Tris-HCl (pH 8.0), 30 mM MgCl2, and 200 mM NaCl. These studies on DNA polymerase encoded by PaP1 help advance our knowledge on phage-encoded DNA polymerases and elucidate PaP1 propagation in infected P. aeruginosa. PMID:27052734

  10. Forensic DNA analysis.

    Science.gov (United States)

    McDonald, Jessica; Lehman, Donald C

    2012-01-01

    Before the routine use of DNA profiling, blood typing was an important forensic tool. However, blood typing was not very discriminating. For example, roughly 30% of the United States population has type A-positive blood. Therefore, if A-positive blood were found at a crime scene, it could have come from 30% of the population. DNA profiling has a much better ability for discrimination. Forensic laboratories no longer routinely determine blood type. If blood is found at a crime scene, DNA profiling is performed. From Jeffrey's discovery of DNA fingerprinting to the development of PCR of STRs to the formation of DNA databases, our knowledge of DNA and DNA profiling have expanded greatly. Also, the applications for which we use DNA profiling have increased. DNA profiling is not just used for criminal case work, but it has expanded to encompass paternity testing, disaster victim identification, monitoring bone marrow transplants, detecting fetal cells in a mother's blood, tracing human history, and a multitude of other areas. The future of DNA profiling looks expansive with the development of newer instrumentation and techniques. PMID:22693781

  11. DNA profiles from fingermarks.

    Science.gov (United States)

    Templeton, Jennifer E L; Linacre, Adrian

    2014-11-01

    Criminal investigations would be considerably improved if DNA profiles could be routinely generated from single fingermarks. Here we report a direct DNA profiling method that was able to generate interpretable profiles from 71% of 170 fingermarks. The data are based on fingermarks from all 5 digits of 34 individuals. DNA was obtained from the fingermarks using a swab moistened with Triton-X, and the fibers were added directly to one of two commercial DNA profiling kits. All profiles were obtained without increasing the number of amplification cycles; therefore, our method is ideally suited for adoption by the forensic science community. We indicate the use of the technique in a criminal case in which a DNA profile was generated from a fingermark on tape that was wrapped around a drug seizure. Our direct DNA profiling approach is rapid and able to generate profiles from touched items when current forensic practices have little chance of success. PMID:25391915

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

    OpenAIRE

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

    2013-01-01

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

  13. Innovations. DNA detectives.

    OpenAIRE

    May, M

    1999-01-01

    To understand the many potential causes and resulting consequences of DNA damage, scientists first need methods to detect it. Canadian scientists X. Chris Le and Michael Weinfeld, with help from U.S. molecular biologist Steven Leadon, developed a selective, sensitive technique for measuring DNA damage. The scientists combined a thymine glycol antibody with thymine glycol to selectively tag a specific type of DNA damage. They then added a second antibody with fluorescing properties, and used l...

  14. The Bacillus subtilis DnaD and DnaB Proteins Exhibit Different DNA Remodelling Activities

    OpenAIRE

    Zhang, Wenke; Carneiro, Maria J. V. M.; Turner, Ian J.; ALLEN, Stephanie; Roberts, Clive J.; Soultanas, Panos

    2005-01-01

    Primosomal protein cascades load the replicative helicase onto DNA. In Bacillus subtilis a putative primosomal cascade involving the DnaD-DnaB-DnaI proteins has been suggested to participate in both the DnaA and PriA-dependent loading of the replicative helicase DnaC onto the DNA. Recently we discovered that DnaD has a global remodelling DNA activity suggesting a more widespread role in bacterial nucleoid architecture. Here, we show that DnaB forms a “square-like” tetramer with a hole in the ...

  15. DNA fingerprinting in botany: past, present, future.

    Science.gov (United States)

    Nybom, Hilde; Weising, Kurt; Rotter, Björn

    2014-01-01

    Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing

  16. DNA Microarray Technique

    Directory of Open Access Journals (Sweden)

    Thakare SP

    2012-11-01

    Full Text Available DNA Microarray is the emerging technique in Biotechnology. The many varieties of DNA microarray or DNA chip devices and systems are described along with their methods for fabrication and their use. It also includes screening and diagnostic applications. The DNA microarray hybridization applications include the important areas of gene expression analysis and genotyping for point mutations, single nucleotide polymorphisms (SNPs, and short tandem repeats (STRs. In addition to the many molecular biological and genomic research uses, this review covers applications of microarray devices and systems for pharmacogenomic research and drug discovery, infectious and genetic disease and cancer diagnostics, and forensic and genetic identification purposes.

  17. DNA ELECTROPHORESIS AT SURFACES

    Energy Technology Data Exchange (ETDEWEB)

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01

    During this year we performed two major projects: I. We developed a detailed theoretical model which complements our experiments on surface DNA electrophoresis. We found that it was possible to enhance the separation of DNA chains by imposing a chemical nanoscale pattern on the surface. This approach utilized the surface interaction effect of the DNA chains with the substrate and is a refinement to our previous method in which DNA chains were separated on homogeneous flat surfaces. By introducing the nano-patterns on the surface, the conformational changes of DNA chains of different lengths can be amplified, which results in the different friction strengths with the substrate surface. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation. II. In collaboration with a large international manufacturer of skin care products we also embarked on a project involving photo toxicity of titanium dioxide nanoparticles, which are a key ingredient in sunscreen and cosmetic lotions. The results clearly implicated the nanoparticles in catalyzing damage to chromosomal DNA. We then used this knowledge to develop a polymer/anti-oxidant coating which prevented the photocatalytic reaction on DNA while still retaining the UV absorptive properties of the nanoparticles. The standard gel electrophoresis was not sufficient in determining the extent of the DNA damage. The conclusions of this study were based predominantly on analysis obtained with the surface electrophoresis method.

  18. DNA methylation in hepatocellular carcinoma

    Institute of Scientific and Technical Information of China (English)

    Iris Tischoff; Andrea Tannapfel

    2008-01-01

    As for many other tumors, development of hepatocellular carcinoma (HCC) must be understood as a multistep process with accumulation of genetic and epigenetic alterations in regulatory genes, leading to activation of oncogenes and inactivation or loss of tumor suppressor genes (TSG). In the last decades, in addition to genetic alterations, epigenetic inactivation of (tumor suppressor) genes by promoter hypermethylation has been recognized as an important and alternative mechanism in tumorigenesis. In HCC, aberrant methylation of promoter sequences occurs not only in advanced tumors, it has been also observed in premalignant conditions just as chronic viral hepatitis B or C and cirrhotic liver. This review discusses the epigenetic alterations in hepatocellular carcinoma focusing DNA methylation.

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

    OpenAIRE

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

    2015-01-01

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

  20. RNA sequencing: advances, challenges and opportunities

    OpenAIRE

    Ozsolak, Fatih; Milos, Patrice M.

    2010-01-01

    In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an even more complete characterization of RNA transcripts. These developments include improvements in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA characterization and detection of alternative spli...

  1. Single cell genomics: advances and future perspectives.

    OpenAIRE

    Macaulay, Iain C.; Thierry Voet

    2014-01-01

    Advances in whole-genome and whole-transcriptome amplification have permitted the sequencing of the minute amounts of DNA and RNA present in a single cell, offering a window into the extent and nature of genomic and transcriptomic heterogeneity which occurs in both normal development and disease. Single-cell approaches stand poised to revolutionise our capacity to understand the scale of genomic, epigenomic, and transcriptomic diversity that occurs during the lifetime of an individual organis...

  2. DNA triple helix formation: A potential tool for genetic repair

    Directory of Open Access Journals (Sweden)

    Nayak A

    2006-01-01

    Full Text Available DNA triple helices offer new perspectives towards oligonucleotide-directed gene regulation. Triple helix forming oligonucleotides, which bind to double-stranded DNA, are of special interest since they are targeted to the gene itself rather than to its mRNA product (as in the antisense strategy. However, the poor stability of some of these structures might limit their use under physiological conditions. Specific ligands can intercalate into DNA triple helices and stabilize them. This review summarizes recent advances in this field while also highlighting major obstacles that remain to be overcome, before the application of triplex technology to therapeutic gene repair can be achieved.

  3. Binding and Transformation of Extracellular DNA in Soil

    Institute of Scientific and Technical Information of China (English)

    CAI Peng; HUANG Qiao-Yun; ZHANG Xue-Wen; CHEN Hao

    2005-01-01

    DNA is the genetic material of various organisms. Extracellular DNA adsorbed or bound on surface-active particles in soils has been shown to persist for long periods against nucleases degradation and still retain the ability to transform competent cells. This paper reviews some recent advances on the binding and transformation of extracellular DNA in soils,which is fundamental to understanding the nature of the soil, regulating biodiversity, and assessing the risk of releasing genetically engineered microorganisms (GEMs) as well as being helpful for development of the genetic evolutional theory of bacteria. Several influencing factors, such as soil pH, ionic strength, soil surface properties, and characteristics of the DNA polymer, are discussed. To date, the understanding of the type of molecular binding sites and the conformation of adsorbed and bound DNA to soil particles is still in its infancy.

  4. Spectroscopic investigation on the telomeric DNA base sequence repeat

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

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

  5. A multi-field approach to DNA condensation

    Science.gov (United States)

    Ran, Shi-Yong; Jia, Jun-Li

    2015-12-01

    DNA condensation is an important process in many fields including life sciences, polymer physics, and applied technology. In the nucleus, DNA is condensed into chromosomes. In polymer physics, DNA is treated as a semi-flexible molecule and a polyelectrolyte. Many agents, including multi-valent cations, surfactants, and neutral poor solvents, can cause DNA condensation, also referred to as coil-globule transition. Moreover, DNA condensation has been used for extraction and gene delivery in applied technology. Many physical theories have been presented to elucidate the mechanism underlying DNA condensation, including the counterion correlation theory, the electrostatic zipper theory, and the hydration force theory. Recently several single-molecule studies have focused on DNA condensation, shedding new light on old concepts. In this document, the multi-field concepts and theories related to DNA condensation are introduced and clarified as well as the advances and considerations of single-molecule DNA condensation experiments are introduced. Project supported by the National Natural Science Foundation of China (Grant Nos. 21204065 and 20934004) and the Natural Science Foundation of Zhejiang Province, China (Grant No. Y4110357).

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

    Science.gov (United States)

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

    2015-10-01

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

  7. cDNA: 53887 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus + Mm.196480 Mus musculus adult male testis cDNA, RIKEN full-length enriched library, ... uct:DNA Segment, Chr 15 Massachusetts Institute of Technology ... 260, full insert sequence gnl|UG|Mm#S10837764 AK07 ...

  8. cDNA: 53885 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus + Mm.196480 Mus musculus adult male testis cDNA, RIKEN full-length enriched library, ... uct:DNA Segment, Chr 15 Massachusetts Institute of Technology ... 260, full insert sequence gnl|UG|Mm#S10837547 AK07 ...

  9. Recombinant DNA for Teachers.

    Science.gov (United States)

    Duvall, James G., III

    1992-01-01

    A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

  10. Characterization of muntjac DNA

    International Nuclear Information System (INIS)

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange

  11. Routine DNA testing

    Science.gov (United States)

    Routine DNA testing. It’s done once you’ve Marker-Assisted Breeding Pipelined promising Qantitative Trait Loci within your own breeding program and thereby established the performance-predictive power of each DNA test for your germplasm under your conditions. By then you are ready to screen your par...

  12. DNA-cell conjugates

    Energy Technology Data Exchange (ETDEWEB)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  13. Extended DNA Tile Actuators

    DEFF Research Database (Denmark)

    Kristiansen, Martin; Kryger, Mille; Zhang, Zhao;

    2012-01-01

    A dynamic linear DNA tile actuator is expanded to three new structures of higher complexity. The original DNA actuator was constructed from a central roller strand which hybridizes with two piston strands by forming two half-crossover junctions. A linear expansion of the actuator is obtained...

  14. Characterization of muntjac DNA

    Energy Technology Data Exchange (ETDEWEB)

    Davis, R.C.

    1981-05-27

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange.

  15. Workshop on DNA repair.

    NARCIS (Netherlands)

    A.R. Lehmann (Alan); J.H.J. Hoeijmakers (Jan); A.A. van Zeeland (Albert); C.M.P. Backendorf (Claude); B.A. Bridges; A. Collins; R.P.D. Fuchs; G.P. Margison; R. Montesano; E. Moustacchi; A.T. Natarajan; M. Radman; A. Sarasin; E. Seeberg; C.A. Smith; M. Stefanini (Miria); L.H. Thompson; G.P. van der Schans; C.A. Weber (Christine); M.Z. Zdzienika

    1992-01-01

    textabstractA workshop on DNA repair with emphasis on eukaryotic systems was held, under the auspices of the EC Concerted Action on DNA Repair and Cancer, at Noordwijkerhout (The Netherlands) 14-19 April 1991. The local organization of the meeting was done under the auspices of the Medical Genetic C

  16. Protein–DNA Interactions

    NARCIS (Netherlands)

    Kovacic, L.; Boelens, R.

    2012-01-01

    The recognition of specific DNA sequences by proteins and the coupling to signaling events are fundamental occurrences that lie at the root of many cellular processes. Many examples of tight control by protein–DNA interactions can be found in such dynamic processes as transcription, replication and

  17. Cellular processing and destinies of artificial DNA nanostructures.

    Science.gov (United States)

    Lee, Di Sheng; Qian, Hang; Tay, Chor Yong; Leong, David Tai

    2016-08-01

    Since many bionanotechnologies are targeted at cells, understanding how and where their interactions occur and the subsequent results of these interactions is important. Changing the intrinsic properties of DNA nanostructures and linking them with interactions presents a holistic and powerful strategy for understanding dual nanostructure-biological systems. With the recent advances in DNA nanotechnology, DNA nanostructures present a great opportunity to understand the often convoluted mass of information pertaining to nanoparticle-biological interactions due to the more precise control over their chemistry, sizes, and shapes. Coupling just some of these designs with an understanding of biological processes is both a challenge and a source of opportunities. Despite continuous advances in the field of DNA nanotechnology, the intracellular fate of DNA nanostructures has remained unclear and controversial. Because understanding its cellular processing and destiny is a necessary prelude to any rational design of exciting and innovative bionanotechnology, in this review, we will discuss and provide a comprehensive picture relevant to the intracellular processing and the fate of various DNA nanostructures which have been remained elusive for some time. We will also link the unique capabilities of DNA to some novel ideas for developing next-generation bionanotechnologies. PMID:27119124

  18. Quantification of DNA by Agarose Gel Electrophoresis and Analysis of the Topoisomers of Plasmid and M13 DNA Following Treatment with a Restriction Endonuclease or DNA Topoisomerase I

    Science.gov (United States)

    Tweedie, John W.; Stowell, Kathryn M.

    2005-01-01

    A two-session laboratory exercise for advanced undergraduate students in biochemistry and molecular biology is described. The first session introduces students to DNA quantification by ultraviolet absorbance and agarose gel electrophoresis followed by ethidium bromide staining. The second session involves treatment of various topological forms of…

  19. Premeltons in DNA.

    Science.gov (United States)

    Sobell, Henry M

    2016-03-01

    Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. They are of two kinds: B-B (or A-A) premeltons form at specific DNA-regions to nucleate site-specific DNA melting. These are stationary and, being globally-nontopological, undergo breather-motions that allow drugs and dyes to intercalate into DNA. B-A (or A-B) premeltons, on the other hand, are mobile, and being globally-topological, act as phase-boundaries transforming B- into A-DNA during the structural phase-transition. They are not expected to undergo breather motions. A key feature of both types of premeltons is the presence of an intermediate structural-form in their central regions (proposed as being a transition-state intermediate in DNA-melting and in the B- to A-transition), which differs from either A- or B-DNA. Called beta-DNA, this is both metastable and hyperflexible-and contains an alternating sugar-puckering pattern along the polymer backbone combined with the partial unstacking (in its lower energy-forms) of every-other base-pair. Beta-DNA is connected to either B- or to A-DNA on either side by boundaries possessing a gradation of nonlinear structural-change, these being called the kink and the antikink regions. The presence of premeltons in DNA leads to a unifying theory to understand much of DNA physical chemistry and molecular biology. In particular, premeltons are predicted to define the 5' and 3' ends of genes in naked-DNA and DNA in active-chromatin, this having important implications for understanding physical aspects of the initiation, elongation and termination of RNA-synthesis during transcription. For these and other reasons, the model will be of broader interest to the general-audience working in these areas. The model explains a wide variety of data, and carries with it a number of experimental predictions-all readily testable-as will be described in this review. PMID

  20. Whose DNA is this?

    DEFF Research Database (Denmark)

    Taroni, Franco; Biedermann, Alex; Vuille, Joëlle;

    2013-01-01

    This communication seeks to draw the attention of researchers and practitioners dealing with forensic DNA profiling analyses to the following question: is a scientist's report, offering support to a hypothesis according to which a particular individual is the source of DNA detected during...... evoked during the international conference "The hidden side of DNA profiles. Artifacts, errors and uncertain evidence" held in Rome (April 27th to 28th, 2012). Indeed, despite the fact that this conference brought together some of the world's leading forensic DNA specialists, it appeared clearly...... talk considerably different languages. It thus is fundamental to address this issue of communication about results of forensic DNA analyses, and open a dialogue with practicing non-scientists at large who need to make meaningful use of scientific results to approach and help solve judicial cases...

  1. Archaeal DNA replication.

    Science.gov (United States)

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed. PMID:25421597

  2. Searching target sites on DNA by proteins: Role of DNA dynamics under confinement

    Science.gov (United States)

    Mondal, Anupam; Bhattacherjee, Arnab

    2015-01-01

    DNA-binding proteins (DBPs) rapidly search and specifically bind to their target sites on genomic DNA in order to trigger many cellular regulatory processes. It has been suggested that the facilitation of search dynamics is achieved by combining 3D diffusion with one-dimensional sliding and hopping dynamics of interacting proteins. Although, recent studies have advanced the knowledge of molecular determinants that affect one-dimensional search efficiency, the role of DNA molecule is poorly understood. In this study, by using coarse-grained simulations, we propose that dynamics of DNA molecule and its degree of confinement due to cellular crowding concertedly regulate its groove geometry and modulate the inter-communication with DBPs. Under weak confinement, DNA dynamics promotes many short, rotation-decoupled sliding events interspersed by hopping dynamics. While this results in faster 1D diffusion, associated probability of missing targets by jumping over them increases. In contrast, strong confinement favours rotation-coupled sliding to locate targets but lacks structural flexibility to achieve desired specificity. By testing under physiological crowding, our study provides a plausible mechanism on how DNA molecule may help in maintaining an optimal balance between fast hopping and rotation-coupled sliding dynamics, to locate target sites rapidly and form specific complexes precisely. PMID:26400158

  3. Nanoparticle bridge DNA biosensor

    Science.gov (United States)

    Huang, Hong-Wen

    A new DNA sensing method is demonstrated in which DNA hybridization events lead to the formation of nanoparticle satellites that bridge two electrodes and are detected electrically. The hybridization events are exclusively carried out only on specific locations, the surfaces of C-ssDNA modified 50 nm GNPs. The uniqueness of this work is that only a small number of T-ccDNA molecules (target DNA and three-base-pair-mismatched DNA in 20nM concentrations. Three single-stranded DNA (ssDNA) system is used in our experiment which includes Capture-ssDNA (C-ssDNA), Target-ssDNA (T-ssDNA) and Probe-ssDNA (P-ssDNA). Both C-ssDNA and P-ssDNA are modified by a thiol group and can hybridize with different portions of T-ssDNA. T-ssDNA requires no modification in three ssDNA system, which is beneficial in many applications. C-ssDNA modified 50nm gold nanoparticle (C-50au) and P-ssDNA modified 30nm gold nanoparticle (P-30au) are prepared through the reaction of thiol-gold chemical bonding between thiolated ssDNA and gold nanoparticle (GNP) (C-ssDNA with 50nm GNP, P-ssDNA with 30nm GNP). We controllably place the C-50au only on the SiO2 band surface (˜ 90nm width) between two gold electrodes (source and drain electrodes) by forming positively- and negatively-charged self-assembled monolayers (SAMs) on SiO2 and gold surface, respectively. DNA modified GNP is negatively charged due to ionization of phosphate group on DNA back bone. C-50au therefore is negatively charged and can only be attracted toward SiO2 area (repelled by negatively charged gold electrode surface). The amine group of positively-charged SAMs on SiO2 surface is then passivated by converting to non-polar methyl functional group after C-50au placement. P-30au is first hybridized with T-ssDNA in the solution phase (T-P- 30au formed) and is introduced into DNA detection device in which C-50au are immobilized on ˜90nm width SiO2 band (between two gold electrodes). The passivation step ensures every TP-30au are attached

  4. DNA Align Editor: DNA Alignment Editor Tool

    Science.gov (United States)

    The SNPAlignEditor is a DNA sequence alignment editor that runs on Windows platforms. The purpose of the program is to provide an intuitive, user-friendly tool for manual editing of multiple sequence alignments by providing functions for input, editing, and output of nucleotide sequence alignments....

  5. Single Molecule Atomic Force Microscopy Studies of Photosensitized Singlet Oxygen Behavior on a DNA Origami Template

    DEFF Research Database (Denmark)

    Helmig, Sarah Wendelboe; Rotaru, Alexandru; Arian, Dumitru;

    2010-01-01

    DNA origami, the folding of a long single-stranded DNA sequence (scaffold strand) by hundreds of short synthetic oligonucleotides (staple strands) into parallel aligned helices, is a highly efficient method to form advanced self-assembled DNA-architectures. Since molecules and various materials can...... a single photosensitizer molecule conjugated to a selected DNA origami staple strand on an origami structure. We demonstrate a distance-dependent oxidation of organic moieties incorporated in specific positions on DNA origami by singlet oxygen produced from a single photosensitizer located at the...

  6. DNA testing in hereditary neuropathies.

    LENUS (Irish Health Repository)

    Murphy, Sinéad M

    2013-01-01

    The inherited neuropathies are a clinically and genetically heterogeneous group of disorders in which there have been rapid advances in the last two decades. Molecular genetic testing is now an integral part of the evaluation of patients with inherited neuropathies. In this chapter we describe the genes responsible for the primary inherited neuropathies. We briefly discuss the clinical phenotype of each of the known inherited neuropathy subgroups, describe algorithms for molecular genetic testing of affected patients and discuss genetic counseling. The basic principles of careful phenotyping, documenting an accurate family history, and testing the available genes in an appropriate manner should identify the vast majority of individuals with CMT1 and many of those with CMT2. In this chapter we also describe the current methods of genetic testing. As advances are made in molecular genetic technologies and improvements are made in bioinformatics, it is likely that the current time-consuming methods of DNA sequencing will give way to quicker and more efficient high-throughput methods, which are briefly discussed here.

  7. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC GENETIC MARKERS IN HUMAN FECAL MICROBIAL COMMUNITIES

    Science.gov (United States)

    Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for mo...

  8. Identification of Bacterial DNA Markers for the Detection of Human and Cattle Fecal Pollution - SLIDES

    Science.gov (United States)

    Technological advances in DNA sequencing and computational biology allow scientists to compare entire microbial genomes. However, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for most laborato...

  9. IDENTIFICATION OF BACTERIAL DNA MARKERS FOR THE DETECTION OF HUMAN AND CATTLE FECAL POLLUTION

    Science.gov (United States)

    Technological advances in DNA sequencing and computational biology allow scientists to compare entire microbial genomes. However, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for most laborato...

  10. Attacking hepatitis B virus cccDNA--The holy grail to hepatitis B cure.

    Science.gov (United States)

    Lucifora, Julie; Protzer, Ulrike

    2016-04-01

    HBV deposits a covalently closed circular DNA form, called cccDNA, in the nucleus of infected cells. As the central transcription template, the cccDNA minichromosome is a key intermediate in the HBV life cycle. Its location in the nucleus makes cccDNA a difficult target for antivirals and immune response, and therefore it is responsible for chronicity of HBV infection. While little is known about the mechanisms involved in cccDNA formation, current research is accumulating data on the mechanisms regulating transcription from cccDNA, and the first potential targeting approaches have been reported. This review will summarize our knowledge about cccDNA biology and the latest advances in cccDNA targeting strategies in order to finally achieve an HBV cure. PMID:27084036

  11. Radiation-induced DNA damage and DNA repair

    International Nuclear Information System (INIS)

    Although DNA undergoes various types of damage from radiation, active oxygen, and the like, a living body has a plurality of DNA repair mechanisms responding to the types of DNA damage. On the other hand, there are a system that results in cell death if the repair is impossible and a mechanism to lead to concretization if further repair is not accurately made. This paper explains the following items as the basic researches on these types of DNA damage and the repair mechanisms: (1) biological effects of DNA damage, (2) effect of DNA damage on DNA synthesis, and (3) effects of DNA damage on cells. It also explains the effects of radiation on cells with a focus on specific mechanism for (1) DNA damage caused by direct action due to radiation and by indirect action due mainly to active oxygen, and (2) DNA repair mechanism that works on DNA double-strand break (DSB). (A.O.)

  12. What Controls DNA Looping?

    Directory of Open Access Journals (Sweden)

    Pamela J. Perez

    2014-08-01

    Full Text Available The looping of DNA provides a means of communication between sequentially distant genomic sites that operate in tandem to express, copy, and repair the information encoded in the DNA base sequence. The short loops implicated in the expression of bacterial genes suggest that molecular factors other than the naturally stiff double helix are involved in bringing the interacting sites into close spatial proximity. New computational techniques that take direct account of the three-dimensional structures and fluctuations of protein and DNA allow us to examine the likely means of enhancing such communication. Here, we describe the application of these approaches to the looping of a 92 base-pair DNA segment between the headpieces of the tetrameric Escherichia coli Lac repressor protein. The distortions of the double helix induced by a second protein—the nonspecific nucleoid protein HU—increase the computed likelihood of looping by several orders of magnitude over that of DNA alone. Large-scale deformations of the repressor, sequence-dependent features in the DNA loop, and deformability of the DNA operators also enhance looping, although to lesser degrees. The correspondence between the predicted looping propensities and the ease of looping derived from gene-expression and single-molecule measurements lends credence to the derived structural picture.

  13. Quantitive DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  14. PREPARATION AND PURIFICATION OF DNA FROM BACTERIAL CELLS; CHARACTERIZATION OF PLASMID DNA

    Directory of Open Access Journals (Sweden)

    M Praveen, G Adarsh, T Ramesh, M Ramesh*

    2013-01-01

    Full Text Available The use of genetic material to deliver genes for therapeutic purposes has been practiced for many years. With the advancement in genetic engineering, foreign genes of industrial applications can be inserted into cloning vector for mass production in various host cells. Escherichia coli is an extremely important model organism in modern biological engineering, the suitable growth media is essential for the optimal expression of the genes in E. coli. The present study aims at isolation and purification of genomic DNA from E. coli, the characterization of pBR322 plasmid DNA. Bacterial culture conditions were optimized in shake – flask cultures based on optimal temperature, inoculum size and medium composition. Solutions and methods are disclosed for the effective, simple isolation of DNA from bacterial cells. High bioprocess recovery and product quality were primarily associated with the complete removal of total cellular RNA impurity. The process was demonstrated without the use of animal-derived RNase. High-molecular-weight (HMW RNA and other impurities were removed by selective precipitation using calcium chloride at an optimal concentration.The optimal conditions for the growth of Escherichia coli were shown maximum absorbance as 7.5 at 370C temperature, 1% inoculum size using TB medium composition. The purified genomic DNA had concentration as 73.5 µg/ml and purity 1.8. The 0.5M CaCl2 was optimal concentration for removal of RNA. The plasmid DNA pBR322 was confirmed by comparing the band to 4.36 Kb, purity of plasmid was 1.85 and it contains 96.8% of super coiled DNA. The contaminants like chromosomal DNA, RNA, host cell proteins and mycoplasma were absent in the plasmid DNA.

  15. DNA-PK assay

    Science.gov (United States)

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12

    The present invention provides a method for detecting DNA-activated protein kinase (DNA-PK) activity in a biological sample. The method includes contacting a biological sample with a detectably-labeled phosphate donor and a synthetic peptide substrate defined by the following features to provide specific recognition and phosphorylation by DNA-PK: (1) a phosphate-accepting amino acid pair which may include serine-glutamine (Ser-Gln) (SQ), threonine-glutamine (Thr-Gln) (TQ), glutamine-serine (Gln-Ser) (QS), or glutamine-threonine (Gln-Thr) (QT); (2) enhancer amino acids which may include glutamic acid or glutamine immediately adjacent at the amino- or carboxyl- side of the amino acid pair and forming an amino acid pair-enhancer unit; (3) a first spacer sequence at the amino terminus of the amino acid pair-enhancer unit; (4) a second spacer sequence at the carboxyl terminus of the amino acid pair-enhancer unit, which spacer sequences may include any combination of amino acids that does not provide a phosphorylation site consensus sequence motif; and, (5) a tag moiety, which may be an amino acid sequence or another chemical entity that permits separating the synthetic peptide from the phosphate donor. A compostion and a kit for the detection of DNA-PK activity are also provided. Methods for detecting DNA, protein phosphatases and substances that alter the activity of DNA-PK are also provided. The present invention also provides a method of monitoring protein kinase and DNA-PK activity in living cells. -A composition and a kit for monitoring protein kinase activity in vitro and a composition and a kit for monitoring DNA-PK activities in living cells are also provided. A method for identifying agents that alter protein kinase activity in vitro and a method for identifying agents that alter DNA-PK activity in living cells are also provided.

  16. Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients

    OpenAIRE

    Wen, Lu; Li, Jingyi; Guo, Huahu; Liu, Xiaomeng; Zheng, Shengmin; Zhang, Dafang; Zhu, Weihua; Qu, Jianhui; Guo, Limin; Du, Dexiao; Jin, Xiao; Zhang, Yuhao; Gao, Yun; Jie SHEN; Ge, Hao

    2015-01-01

    Despite advances in DNA methylome analyses of cells and tissues, current techniques for genome-scale profiling of DNA methylation in circulating cell-free DNA (ccfDNA) remain limited. Here we describe a methylated CpG tandems amplification and sequencing (MCTA-Seq) method that can detect thousands of hypermethylated CpG islands simultaneously in ccfDNA. This highly sensitive technique can work with genomic DNA as little as 7.5 pg, which is equivalent to 2.5 copies of the haploid genome. We ha...

  17. "Artifactual" arsenate DNA

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2012-01-01

    The recent claim by Wolfe-Simon et al. that the Halomonas bacterial strain GFAJ-1 when grown in arsenate-containing medium with limiting phosphate is able to substitute phosphate with arsenate in biomolecules including nucleic acids and in particular DNA(1) arose much skepticism, primarily due...... to the very limited chemical stability of arsenate esters (see ref. 2 and references therein). A major part of the criticisms was concerned with the insufficient (bio)chemical evidence in the Wolfe-Simon study for the actual chemical incorporation of arsenate in DNA (and/or RNA). Redfield et al. now present...... evidence that the identification of arsenate DNA was artifactual....

  18. DNA fusion gene vaccines

    DEFF Research Database (Denmark)

    Holst, Peter Johannes; Bassi, Maria Rosaria; Thomsen, Allan Randrup;

    2010-01-01

    DNA vaccines are versatile and safe, but limited immunogenicity has prevented their use in the clinical setting. Experimentally, immunogenicity may be enhanced by the use of new delivery technologies, by coadministration of cytokines and pathogen-associated molecular patterns, or by fusion...... with these modifications, it is likely that the primary use of DNA vaccines may be as primers for viral-vectored vaccines, rather than as single agents. This review discusses the approaches used to enhance DNA vaccine immunogenicity, with a primary focus on fusion strategies that enhance antigen presentation....

  19. Apoptosis and DNA Methylation

    Directory of Open Access Journals (Sweden)

    Richard R. Meehan

    2011-04-01

    Full Text Available Epigenetic mechanisms assist in maintaining gene expression patterns and cellular properties in developing and adult tissues. The molecular pathology of disease states frequently includes perturbation of DNA and histone methylation patterns, which can activate apoptotic pathways associated with maintenance of genome integrity. This perspective focuses on the pathways linking DNA methyltransferases and methyl-CpG binding proteins to apoptosis, and includes new bioinformatic analyses to characterize the evolutionary origin of two G/T mismatch-specific thymine DNA glycosylases, MBD4 and TDG.

  20. Recent advances of aptamer sensors

    Institute of Scientific and Technical Information of China (English)

    LI YiLin; GUO Lei; ZHANG ZhaoYang; TANG JiJun; XIE JianWei

    2008-01-01

    Aptamers are a series of high-affinity and high-specificity oligoneucleotides (single-stranded DNA or RNA) to the target, usually selected by the combinatorial chemistry SELEX technique (systematic evolution of ligands by exponential enrichment). Aptamers have proved to be one kind of novel func-tional molecules in life science and chemistry. After being labeled by signaling groups, the aptamer probe can conveniently transfer the characteristics of aptamer-target recognition to a form of high-sensitive signal, and the high-affinity, high-specificity measurements of metal ion, organic mole-cules, nucleic acid, proteins, or cells become possible. This article summarizes the recent advances of aptamer probes in different sensing fields, with special emphasis on aptamer probes as fluorescent sensors.

  1. Recent advances of aptamer sensors

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Aptamers are a series of high-affinity and high-specificity oligoneucleotides (single-stranded DNA or RNA) to the target, usually selected by the combinatorial chemistry SELEX technique (systematic evolution of ligands by exponential enrichment). Aptamers have proved to be one kind of novel functional molecules in life science and chemistry. After being labeled by signaling groups, the aptamer probe can conveniently transfer the characteristics of aptamer-target recognition to a form of high-sensitive signal, and the high-affinity, high-specificity measurements of metal ion, organic molecules, nucleic acid, proteins, or cells become possible. This article summarizes the recent advances of aptamer probes in different sensing fields, with special emphasis on aptamer probes as fluorescent sensors.

  2. Improved immobilization of DNA to microwell plates for DNA-DNA hybridization.

    OpenAIRE

    Hirayama, H.; Tamaoka, J; Horikoshi, K

    1996-01-01

    An improved and simplified protocol for DNA immobilization was developed to enhance DNA-DNA hybridization on microwell plates. Target DNA was immobilized by simple dry-adsorption. Efficiencies of DNA immobilization and retention were enhanced 1.4-6.5 times and 4.2-19.6 times, respectively, compared with a conventional method. The overall hybridization efficiency was increased 3.1-5.2 times. This simple new protocol can reduce the consumption of scarce DNA samples.

  3. Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples

    Science.gov (United States)

    Pilliod, David S.; Goldberg, Caren S.; Arkle, Robert S.; Waits, Lisette P.

    2013-01-01

    Environmental DNA (eDNA) methods for detecting aquatic species are advancing rapidly, but with little evaluation of field protocols or precision of resulting estimates. We compared sampling results from traditional field methods with eDNA methods for two amphibians in 13 streams in central Idaho, USA. We also evaluated three water collection protocols and the influence of sampling location, time of day, and distance from animals on eDNA concentration in the water. We found no difference in detection or amount of eDNA among water collection protocols. eDNA methods had slightly higher detection rates than traditional field methods, particularly when species occurred at low densities. eDNA concentration was positively related to field-measured density, biomass, and proportion of transects occupied. Precision of eDNA-based abundance estimates increased with the amount of eDNA in the water and the number of replicate subsamples collected. eDNA concentration did not vary significantly with sample location in the stream, time of day, or distance downstream from animals. Our results further advance the implementation of eDNA methods for monitoring aquatic vertebrates in stream habitats.

  4. Forensic Analysis of Canine DNA Samples in the Undergraduate Biochemistry Laboratory

    Science.gov (United States)

    Carson, Tobin M.; Bradley, Sharonda Q.; Fekete, Brenda L.; Millard, Julie T.; LaRiviere, Frederick J.

    2009-01-01

    Recent advances in canine genomics have allowed the development of highly distinguishing methods of analysis for both nuclear and mitochondrial DNA. We describe a laboratory exercise suitable for an undergraduate biochemistry course in which the polymerase chain reaction is used to amplify hypervariable regions of DNA from dog hair and saliva…

  5. A semi-automated protocol for Archaea DNA extraction from stools.

    OpenAIRE

    Khelaifia, Saber; Ramonet, Pierre-Yves; Bedotto Buffet, Marielle; Drancourt, Michel

    2013-01-01

    BACKGROUND: The PCR-based detection of archaea DNA in human specimens relies on efficient DNA extraction. We previously designed one such protocol involving only manual steps. In an effort to reduce the workload involved, we compared this manual protocol to semi-automated and automated protocols for archaea DNA extraction from human specimens. FINDINGS: We tested 110 human stool specimens using each protocol. An automated protocol using the EZ1 Advanced XL extractor with the V 1.066069118 Qia...

  6. Tissue mitochondrial DNA changes. A stochastic system.

    Science.gov (United States)

    Kopsidas, G; Kovalenko, S A; Heffernan, D R; Yarovaya, N; Kramarova, L; Stojanovski, D; Borg, J; Islam, M M; Caragounis, A; Linnane, A W

    2000-06-01

    Several lines of evidence support the view that the bioenergetic function of the mitochondria in postmitotic tissue deteriorates during normal aging. Skeletal muscle is one such tissue that undergoes age-related fiber loss and atrophy and an age-associated rise in the number of cytochrome c oxidase (COX) deficient fibers. With such metabolic pressure placed on skeletal muscle it would be an obvious advantage to supplement the cellular requirement for energy by up-regulating glycolysis, and alternative pathway for energy synthesis. Analysis of rat skeletal muscle utilizing antibodies directed against key enzymes involved in glycolysis has provided evidence of an age-associated increase in the enzymes involved in glycolysis. Fructose-6-phosphate kinase, aldolase, glyceraldehyde-3-phosphate dehydrogenase, and pyruvate kinase protein levels appeared to increase in the soleus, gracilis, and quadriceps muscle from aged rats. The increase in the level of these proteins appeared to correlate to a corresponding decrease in the amount of cytochrome c oxidase protein measured in the same tissue. Together these results are interpreted to represent a general upregulation of glycolysis that occurs in response to the age-associated decrease in mitochondrial energy capacity. Mitochondrial DNA (mtDNA) damage and mutations may accumulate with advancing age until they reach a threshold level were they impinge on the bioenergy capacity of the cell or tissue. Evidence indicates that mtDNA from the skeletal muscle of both aged rats and humans not only undergoes changes at the nucleotide sequence level (mutations and DNA damage), but also undergoes modifications at the tertiary level to generate unique age-related conformational mtDNA species. One particular age-related conformational form was only detected in aged rat tissues with high demands on respiration, specifically in heart, kidney, soleus muscle, and, to a lesser extent, the quadriceps muscle. The age-related form was not

  7. The review of recent advances in fish genetics and biotechnology

    OpenAIRE

    Mgbabu , Christopher Nwokwa

    2012-01-01

    Great advances have been, and are being made in our knowledge of the genetics and molecular biology (including genomics, proteomics and structural biology). Global molecular profiling technologies such as microassays using DNA or oligonucleotide chip, and protein and lipid chips are being developed. The application of such biotechnological advances are inevitable in aquaculture in the areas of improvement of aquaculture stocks where many molecular markers such as RFLPs, AFLDs and RAPD are now...

  8. DNA synthesis on discontinuous templates by human DNA polymerases: implications for non-homologous DNA recombination.

    OpenAIRE

    Islas, L; Fairley, C F; Morgan, W. F.

    1998-01-01

    DNA polymerases catalyze the synthesis of DNA using a continuous uninterrupted template strand. However, it has been shown that a 3'-->5' exonuclease-deficient form of the Klenow fragment of Escherichia coli DNA polymerase I as well as DNA polymerase of Thermus aquaticus can synthesize DNA across two unlinked DNA templates. In this study, we used an oligonucleotide-based assay to show that discontinuous DNA synthesis was present in HeLa cell extracts. DNA synthesis inhibitor studies as well a...

  9. Expansion of the DNA Alphabet beyond Natural DNA Recognition.

    Science.gov (United States)

    Tateishi-Karimata, Hisae; Sugimoto, Naoki

    2016-07-15

    Simple and inexpensive DNA fibres: New, stable DNA structures are created by the binding of a small molecule to poly(A). Because these DNA fibres are formed from inexpensive materials by using very simple methods, DNA materials suitable for practical use such as information storage should be possible in the near future. PMID:27061868

  10. Phenothiazine as new oxidizable label for electrochemical detection of DNA

    Czech Academy of Sciences Publication Activity Database

    Simonova, Anna; Fojta, Miroslav; Hocek, Michal

    Praha: Czech Chemical Society, 2015. s. 137. [Liblice 2015. Advances in Organic, Bioorganic and Pharmaceutical Chemistry /50./. 06.11.2015-08.11.2015, Olomouc] R&D Projects: GA ČR GBP206/12/G151 Institutional support: RVO:61388963 ; RVO:68081707 Keywords : DNA * electrochemistry * phenothiazine Subject RIV: CC - Organic Chemistry

  11. DNA from soil mirrors plant taxonomic and growth form diversity

    DEFF Research Database (Denmark)

    Yoccoz, N.G.; Bråthen, K.A.; Gielly, L.;

    2012-01-01

    Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call...

  12. PCR synthesis of base-modified DNA templates for transcription

    Czech Academy of Sciences Publication Activity Database

    Raindlová, Veronika; Hocek, Michal

    Praha : Czech Chemical Society, 2015. s. 132. [Liblice 2015. Advances in Organic , Bioorganic and Pharmaceutical Chemistry /50./. 06.11.2015-08.11.2015, Olomouc] R&D Projects: GA ČR GA14-04289S Institutional support: RVO:61388963 Keywords : base-modified DNA * polymerase chain reaction * RNA polymerase Subject RIV: CC - Organic Chemistry

  13. Cleavage of guanine-modified DNA by restriction endonucleases

    Czech Academy of Sciences Publication Activity Database

    Slavíčková, Michaela; Boháčová, Soňa; Perlíková, Pavla; Hocek, Michal

    Praha : Czech Chemical Society, 2015. s. 139. [Liblice 2015. Advances in Organic , Bioorganic and Pharmaceutical Chemistry /50./. 06.11.2015-08.11.2015, Olomouc] R&D Projects: GA ČR GA14-04289S Institutional support: RVO:61388963 Keywords : base-modified DNA * restriction endonucleases Subject RIV: CC - Organic Chemistry

  14. DNA computing in microreactors

    Science.gov (United States)

    Wagler, Patrick; van Noort, Danny; McCaskill, John S.

    2001-11-01

    The goal of this research is to improve the modular stability and programmability of DNA-based computers and in a second step towards optical programmable DNA computing. The main focus here is on hydrodynamic stability. Clockable microreactors can be connected in various ways to solve combinatorial optimisation problems, such as Maximum Clique or 3-SAT. This work demonstrates by construction how one micro-reactor design can be programmed to solve any instance of Maximum Clique up to its given maximum size (N). It reports on an implementation of the architecture proposed previously. This contrasts with conventional DNA computing where the individual sequence of biochemical operations depends on the specific problem. In this pilot study we are tackling a graph for the Maximum Clique problem with NDNA solution space will be presented, which is symbolized by a set of bit-strings (words).

  15. Harnessing DNA intercalation.

    Science.gov (United States)

    Persil, Ozgül; Hud, Nicholas V

    2007-10-01

    Numerous small molecules are known to bind to DNA through base pair intercalation. Fluorescent dyes commonly used for nucleic acid staining, such as ethidium, are familiar examples. Biological and physical studies of DNA intercalation have historically been motivated by mutation and drug discovery research. However, this same mode of binding is now being harnessed for the creation of novel molecular assemblies. Recent studies have used DNA scaffolds and intercalators to construct supramolecular assemblies that function as fluorescent 'nanotags' for cell labeling. Other studies have demonstrated how intercalators can be used to promote the formation of otherwise unstable nucleic acid assemblies. These applications illustrate how intercalators can be used to facilitate and expand DNA-based nanotechnology. PMID:17825446

  16. FBI's DNA analysis program

    Science.gov (United States)

    Brown, John R.

    1994-03-01

    Forensic DNA profiling technology is a significant law enforcement tool due to its superior discriminating power. Applying the principles of population genetics to the DNA profile obtained in violent crime investigations results in low frequency of occurrence estimates for the DNA profile. These estimates often range from a frequency of occurrence of 1 in 50 unrelated individuals to 1 in a million unrelated individuals or even smaller. It is this power to discriminate among individuals in the population that has propelled forensic DNA technology to the forefront of forensic testing in violent crime cases. Not only is the technology extremely powerful in including or excluding a criminal suspect as the perpetrator, but it also gives rise to the potential of identifying criminal suspects in cases where the investigators of unknown suspect cases have exhausted all other available leads.

  17. cDNA: 34099 [

    Lifescience Database Archive (English)

    Full Text Available H. sapiens + Hs.15282 Homo sapiens cDNA FLJ44214 fis, clone THYMU3003309, moderately similar to ... Homo sapiens sarcoma antigen (SAGE ) gnl|UG|Hs#S16886502 AK126202 23/5622_34099.png ...

  18. cDNA: 43397 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus + Mm.30035 Mus musculus adult male corpora quadrigemina cDNA, RIKEN full-length enri ... FOLATE DEHYDROGENASE (EC 1.5.1.6) (10-FTHFDH) (FBP-CI ) homolog [Rattus norvegicus], full insert sequence ...

  19. DNA Sampling Hook

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The DNA Sampling Hook is a significant improvement on a method of obtaining a tissue sample from a live fish in situ from an aquatic environment. A tissue sample...

  20. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

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

    1991-06-19

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

  1. cDNA: 33377 [

    Lifescience Database Archive (English)

    Full Text Available H. sapiens + Hs.181243 Homo sapiens full open reading frame cDNA clone RZPDo834H102D for gene AT ... F4, activating transcription factor 4 (tax -responsive enhancer element B67); complete cds; wi ...

  2. cDNA: 17527 [

    Lifescience Database Archive (English)

    Full Text Available H. sapiens + Hs.134229 Homo sapiens cDNA FLJ44146 fis, clone THYMU2027734, weakly similar to Hom ... o sapiens SA hypertension -associated homolog (rat) (SAH) gnl|UG|Hs#S16886570 ...

  3. cDNA: 47992 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.228067 Mus musculus 15 days embryo male testis cDNA, RIKEN full-length enriched ... lone:8030476B22 product:hypothetical Mitochondrial energy ... transfer proteins (carrier protein) containing pro ...

  4. cDNA: 40711 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus + Mm.41523 Mus musculus adult male thymus cDNA, RIKEN full-length enriched library, ... lone:5830492N08 product:hypothetical Mitochondrial energy ... transfer proteins (carrier protein) containing pro ...

  5. cDNA: 47994 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.228067 Mus musculus 0 day neonate eyeball cDNA, RIKEN full-length enriched libr ... lone:E130118D21 product:hypothetical Mitochondrial energy ... transfer proteins (carrier protein) containing pro ...

  6. cDNA: 47991 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.228067 Mus musculus adult male diencephalon cDNA, RIKEN full-length enriched li ... lone:9330189G22 product:hypothetical Mitochondrial energy ... transfer proteins (carrier protein) containing pro ...

  7. DNA from keratinous tissue

    DEFF Research Database (Denmark)

    Bengtsson, Camilla Friis; Olsen, Maia E.; Brandt, Luise Ørsted;

    2012-01-01

    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...

  8. DNA from keratinous tissue

    DEFF Research Database (Denmark)

    Bengtsson, Camilla F.; Olsen, Maja E.; Brandt, Luise Ørsted;

    2011-01-01

    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...

  9. Making DNA Fingerprints.

    Science.gov (United States)

    Nunley, Kathie F.

    1996-01-01

    Presents an activity to simulate electrophoresis using everyday items. Uses adding machine paper to construct a set of DNA fingerprints that can be used to solve crime cases designed by students in any biology class. (JRH)

  10. cDNA: 36928 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.240850 Mus musculus adult male medulla oblongata cDNA, RIKEN full-length enrich ... MA AMPLIFIED SEQUENCE 1 (NOVEL AMPLIFIED IN BREAST CANCER ... 1) (AMPLIFIED AND OVEREXPRESSED IN BREAST CANCER ) ...

  11. cDNA: 36927 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.240850 Mus musculus adult male stomach cDNA, RIKEN full-length enriched library ... MA AMPLIFIED SEQUENCE 1 (NOVEL AMPLIFIED IN BREAST CANCER ... 1) (AMPLIFIED AND OVEREXPRESSED IN BREAST CANCER ) ...

  12. cDNA: 40220 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.207654 Mus musculus adult male olfactory brain ... cDNA, RIKEN full-length enriched ... library, clone:6430704M03 product:similar to BRAIN ... PROTEIN (FRAGMENT) [Homo sapiens], full insert seq ...

  13. cDNA: 52275 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.275648 Mus musculus 11 days embryo head cDNA, RIKEN full-length enriched librar ... y, clone:6230400I01 product:SIMILAR TO ENIGMA ... (LIM DOMAIN PROTEIN) homolog [Homo sapiens], full ...

  14. cDNA: 52278 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.275648 Mus musculus adult male tongue cDNA, RIKEN full-length enriched library, ... clone:2310073F10 product:SIMILAR TO ENIGMA ... (LIM DOMAIN PROTEIN) homolog [Homo sapiens], full ...

  15. cDNA: 52277 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.275648 Mus musculus 18-day embryo whole body cDNA, RIKEN full-length enriched l ... ibrary, clone:1110003B01 product:SIMILAR TO ENIGMA ... (LIM DOMAIN PROTEIN) homolog [Homo sapiens], full ...

  16. cDNA: 52276 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.275648 Mus musculus adult male brain cDNA, RIKEN full-length enriched library, ... clone:0710007K04 product:SIMILAR TO ENIGMA ... (LIM DOMAIN PROTEIN) homolog [Homo sapiens], full ...

  17. DNA damage and carcinogenesis

    International Nuclear Information System (INIS)

    Although cancer may arise as a result of many different types of molecular changes, there is little reason to doubt that changes to DNA are one of the more important ones in cancer initiation. Although DNA repair mechanisms seem able to eliminate a very large fraction of deleterious changes to DNA, we not only have little insight into the molecular mechanisms involved in such repair, but have a negligible amount of information to permit us to estimate the shape of dose response relations at low doses. The case of skin cancer is a special one, in that the average population is exposed to sufficient solar uv so that the effects of small increments in uv dose may be estimated. An approximate 85% reduction in DNA repair increases skin cancer incidence 104 fold

  18. Kink solitons in DNA

    CERN Document Server

    Zdravković, S; Daniel, M

    2012-01-01

    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.

  19. Mitochondrial DNA homeostasis is essential for nigrostriatal integrity.

    Science.gov (United States)

    Tzoulis, Charalampos; Schwarzlmüller, Thomas; Biermann, Martin; Haugarvoll, Kristoffer; Bindoff, Laurence A

    2016-05-01

    Mitochondrial involvement in the pathogenesis of Parkinson's disease has been suggested by multiple studies, but the mechanisms involved remain unresolved. Here, we sought to identify which mitochondrial defects are associated with degeneration of the nigrostriatal system. Nigrostriatal integrity was assessed in vivo by dopamine transporter (DAT) imaging in twenty-one patients with mitochondrial disorders of different molecular aetiology including: maternally inherited mitochondrial DNA (mtDNA) point mutations, primary single mtDNA deletions, nuclear-encoded disorders of mtDNA replication and maintenance due to mutations in POLG or C10orf2 (Twinkle), and mutations in other nuclear mitochondrial genes including the mitochondrial aspartyl-tRNA synthetase (DARS2) and ADCK3 genes. Patients with mitochondrial disease were compared with twenty patients with Parkinson's disease and eighteen controls. Nigrostriatal degeneration occurred exclusively in patients with defective mtDNA replication and maintenance. In these patients, nigrostriatal degeneration was progressive and at least as severe as in patients with advanced Parkinson's disease. None of the patients with other mitochondrial defects showed evidence of nigral involvement. Our findings demonstrate that dopaminergic neurons of the substantia nigra are specifically vulnerable to defective mtDNA replication/repair or quality control and not to primary point mutations of mtDNA. These results support the hypothesis that accumulating somatic mtDNA damage plays an important role in neurodegeneration. PMID:26979109

  20. Patterning nanocrystals using DNA

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Shara Carol

    2003-09-01

    One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made.[1] Here, we have sought to assemble larger and more complex nanostructures. Gold-DNA conjugates with 50 to 100 bases self-assembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure [2][3] that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA ''trimer.'' This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices

  1. Advances in chemical physics

    CERN Document Server

    Prigogine, Ilya

    2009-01-01

    The Advances in Chemical Physics series provides the chemical physics and physical chemistry fields with a forum for critical, authoritative evaluations of advances in every area of the discipline. Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series serves as the perfect supplement to any advanced graduate class devoted to the study of chemical physics.

  2. DNA-mediated gene transfer without carrier DNA

    OpenAIRE

    1981-01-01

    DNA-mediated gene transfer is a procedure which uses purified DNA to introduce new genetic elements into cells in culture. The standard DNA- mediated gene transfer procedure involves the use of whole cell DNA as carrier DNA for the transfer. We have modified the standard DNA- mediated gene transfer procedure to transfer the Herpes simplex virus type 1 thymidine kinase gene (TK) into TK- murine recipient cells in the absence of whole cell carrier DNA. The majority (8/10) of carrier- free trans...

  3. Electroeluting DNA Fragments

    OpenAIRE

    Zarzosa-Álvarez, Ana L.; Sandoval-Cabrera, Antonio; Torres-Huerta, Ana L.; Ma. Bermudez-Cruz, Rosa

    2010-01-01

    Purified DNA fragments are used for different purposes in Molecular Biology and they can be prepared by several procedures. Most of them require a previous electrophoresis of the DNA fragments in order to separate the band of interest. Then, this band is excised out from an agarose or acrylamide gel and purified by using either: binding and elution from glass or silica particles, DEAE-cellulose membranes, "crush and soak method", electroelution or very often expensive commercial purification ...

  4. DNA-Origami

    DEFF Research Database (Denmark)

    Voigt, Niels Vinther; Tørring, Thomas; Gothelf, Kurt Vesterager

    2010-01-01

    DNA-nanostrukturer giver nye muligheder for studier af individuelle molekyler. Ved at udnytte DNAs unikke selvsamlende egenskaber kan man designe systemer, hvorpå der kan studeres kemiske reaktioner, fluoroforer og biiomolekyler på enkeltmolekyle-niveau.......DNA-nanostrukturer giver nye muligheder for studier af individuelle molekyler. Ved at udnytte DNAs unikke selvsamlende egenskaber kan man designe systemer, hvorpå der kan studeres kemiske reaktioner, fluoroforer og biiomolekyler på enkeltmolekyle-niveau....

  5. An allosteric synthetic DNA.

    OpenAIRE

    Wu, L.; Curran, J F

    1999-01-01

    Allosteric DNA oligonucleotides are potentially useful diagnostic reagents. Here we develop a model system for the study of allosteric interactions in DNAs. A DNA that binds either Cibacron blue or cholic acid was isolated and partially characterized. Isolation was performed using a multi-stage SELEX. First, short oligos that bind either Cibacron blue or cholic acid were enriched from random oligonucleotide pools. Then, members of the two pools were fused to form longer oligos, which were the...

  6. DNA Replication Origins

    OpenAIRE

    Leonard, Alan C.; Méchali, Marcel

    2013-01-01

    The onset of genomic DNA synthesis requires precise interactions of specialized initiator proteins with DNA at sites where the replication machinery can be loaded. These sites, defined as replication origins, are found at a few unique locations in all of the prokaryotic chromosomes examined so far. However, replication origins are dispersed among tens of thousands of loci in metazoan chromosomes, thereby raising questions regarding the role of specific nucleotide sequences and chromatin envir...

  7. Analysis of DNA

    OpenAIRE

    Fiala, Tomáš

    2011-01-01

    Summary This bachelor thesis focuses on the actual use of DNA analysis. The emphasis will be placed mainly on DNA databases of Czech Republic and United Kingdom. Both systems have their own specific characteristics that significantly differ one from the other. Some of those characteristics could be considered to be advantages while other rather as disadvantages mainly with regard to the right for privacy. Therefore, will be introduction of the topic (as well as its historical development)...

  8. Diamondoid-modified DNA

    OpenAIRE

    Wang, Yan; Tkachenko, Boryslav A.; Schreiner, Peter R.; Marx, Andreas

    2011-01-01

    We prepared novel C5-modified triphosphates and phosphoramidites with a diamondoid functionally linked to the nucleobase. Using primer extension experiments with different length templates we investigated whether the modified triphosphates were enzymatically incorporated into DNA and whether they were further extended. We found that all three modified nucleotides can be incorporated into DNA using a single-nucleotide incorporation experiment, but only partially using two templates that demand...

  9. Ejer jeg mit DNA?

    DEFF Research Database (Denmark)

    Hoffmeyer, Jesper

    2010-01-01

    Havasupai-indianerne har så lidt som nogen andre mennesker selv frembragt deres DNA. Det repræsenterer en form for biologisk viden opsamlet gennem milliuoner af års forhistorie......Havasupai-indianerne har så lidt som nogen andre mennesker selv frembragt deres DNA. Det repræsenterer en form for biologisk viden opsamlet gennem milliuoner af års forhistorie...

  10. Photofootprinting of DNA triplexes.

    OpenAIRE

    Lyamichev, V I; Voloshin, O N; Frank-Kamenetskii, M D; Soyfer, V N

    1991-01-01

    We have used a photofootprinting assay to study intermolecular and intramolecular DNA triplexes. The assay is based on the fact that the DNA duplex is protected against photodamage (specifically, against the formation of the (6-4) pyrimidine photoproducts) within a triplex structure. We have shown that this is the case for PyPuPu (YRR) as well as PyPuPy (YRY) triplexes. Using the photofootprinting assay, we have studied the triplex formation under a variety of experimentally defined condition...

  11. What Controls DNA Looping?

    OpenAIRE

    Perez, Pamela J.; Nicolas Clauvelin; Grosner, Michael A.; Colasanti, Andrew V.; Olson, Wilma K.

    2014-01-01

    The looping of DNA provides a means of communication between sequentially distant genomic sites that operate in tandem to express, copy, and repair the information encoded in the DNA base sequence. The short loops implicated in the expression of bacterial genes suggest that molecular factors other than the naturally stiff double helix are involved in bringing the interacting sites into close spatial proximity. New computational techniques that take direct account of the three-dimensional stru...

  12. PDA: Pooled DNA analyzer

    Directory of Open Access Journals (Sweden)

    Lin Chin-Yu

    2006-04-01

    Full Text Available Abstract Background Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer, to analyze pooled DNA data. Results We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB® language, but it can also be executed on a Windows system without installing the MATLAB®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. Conclusion PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.

  13. Abeceda struktur DNA

    Czech Academy of Sciences Publication Activity Database

    Vorlíčková, Michaela

    České Budějovice, 2003. s. 57. [Symposium teoretické a aplikované biofyziky. 18.09.2003-20.09.2003, České Budějovice] R&D Projects: GA AV ČR IAA4004201; GA ČR GA204/01/0561 Institutional research plan: CEZ:AV0Z5004920 Keywords : DNA structures * microsatellite DNA Subject RIV: BO - Biophysics

  14. Introduction to DNA methods

    International Nuclear Information System (INIS)

    The purpose of this session is to discuss the various possibilities for detecting modifications in DNA after irradiation and whether these changes can be utilized as an indicator for the irradiation treatment of foods. The requirement to be fulfilled is that the method be able to distinguish irradiated food without the presence of a control sample, thus the measured response after irradiation must be large enough to supersede background levels from other treatments. Much work has been performed on the effects of radiation on DNA, particularly due to its importance in radiation biology. The main lesions of DNA as a result of irradiation are base damage, damage of the sugar moiety, single strand and double strand breaks. Crosslinking between bases also occurs, e.g. production of thymine dimers, or between DNA and protein. A valuable review on how to utilize these DNA changes for detection purposes has already appeared. Tables 1, 2 and 3 list the proposed methods of detecting changes in irradiated DNA, some identified products as examples for a possible irradiation indicator, in the case of immunoassay the substance used as antigen, and some selected literature references. In this short review, it is not intended to provide a complete literature survey

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

    OpenAIRE

    Halpin, David R; Pehr B Harbury

    2004-01-01

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

  16. DNA-catalyzed sequence-specific hydrolysis of DNA

    OpenAIRE

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

    2009-01-01

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

  17. Origin DNA Melting and Unwinding in DNA Replication

    OpenAIRE

    Gai, Dahai; Chang, Y Paul; Chen, Xiaojiang S.

    2010-01-01

    Genomic DNA replication is a necessary step in the life cycles of all organisms. To initiate DNA replication, the double-stranded DNA (dsDNA) at the origin of replication must be separated or melted; this melted region is propagated and a mature replication fork is formed. To accomplish origin recognition, initial DNA melting, and the eventual formation of a replication fork, coordinated activity of initiators, helicases, and other cellular factors are required. In this review, we focus on re...

  18. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

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

  19. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

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

  20. ACR-700 advanced technologies

    International Nuclear Information System (INIS)

    A successful advanced reactor plant will have optimized economics including reduced operating and maintenance costs, improved performance, and enhanced safety. Incorporating improvements based on advanced technologies ensures cost, safety and operational competitiveness of the ACR-700. These advanced technologies include modern configuration management; construction technologies; operational technology for the control centre and information systems for plant monitoring and analysis. This paper summarizes the advanced technologies used to achieve construction and operational improvements to enhance plant economic competitiveness, advances in the operational technology used for reactor control, and presents the development of the Smart CANDU suite of tools and its application to existing operating reactors and to the ACR-700. (author)

  1. Advances in chemical physics

    CERN Document Server

    Rice, Stuart A

    2012-01-01

    The Advances in Chemical Physics series-the cutting edge of research in chemical physics The Advances in Chemical Physics series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series serves as the perfect supplement to any advanced graduate class devoted to the study of chemical physics. This volume explores: Quantum Dynamical Resonances in Ch

  2. Advances in chemical physics

    CERN Document Server

    Rice, Stuart A

    2012-01-01

    The Advances in Chemical Physics series-the cutting edge of research in chemical physics The Advances in Chemical Physics series provides the chemical physics and physical chemistry fields with a forum for critical, authoritative evaluations of advances in every area of the discipline. Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series presents contributions from internationally renowned chemists and serves as the perfect supplement to any advanced graduate class devoted to the study o

  3. Advanced information society (12)

    Science.gov (United States)

    Komatsuzaki, Seisuke

    In this paper, the original Japanese idea of "advanced information society" was reviewed at the first step. Thus, advancement of information/communication technology, advancement of information/communication needs and tendency of industrialization of information" were examined. Next, by comparing studies on advanced information society in various countries, the Japanese characteristics of consensus building was reviewed. Finally, in pursuit of prospect and tasks for the society, advancement of innovation and convergence information/communication technology, information/communication needs, institutional environment for utilization of information/communication and countermeasures against information pollution. Matching of information/communication technology and needs, besides with countermeasures against information pollution were discussed.

  4. Advances in chemical physics

    CERN Document Server

    Rice, Stuart A

    2011-01-01

    The Advances in Chemical Physics series-the cutting edge of research in chemical physics The Advances in Chemical Physics series provides the chemical physics and physical chemistry fields with a forum for critical, authoritative evaluations of advances in every area of the discipline. Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series offers contributions from internationally renowned chemists and serves as the perfect supplement to any advanced graduate class devoted to the study of che

  5. Advances in chemical Physics

    CERN Document Server

    Rice, Stuart A

    2011-01-01

    The Advances in Chemical Physics series-the cutting edge of research in chemical physics The Advances in Chemical Physics series provides the chemical physics and physical chemistry fields with a forum for critical, authoritative evaluations of advances in every area of the discipline. Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series offers contributions from internationally renowned chemists and serves as the perfect supplement to any advanced graduate class devoted to the study of che

  6. DNA Nanotechnology for Cancer Therapy

    OpenAIRE

    Kumar, Vinit; Palazzolo, Stefano; Bayda, Samer; Corona, Giuseppe; Toffoli, Giuseppe; Rizzolio, Flavio

    2016-01-01

    DNA nanotechnology is an emerging and exciting field, and represents a forefront frontier for the biomedical field. The specificity of the interactions between complementary base pairs makes DNA an incredible building material for programmable and very versatile two- and three-dimensional nanostructures called DNA origami. Here, we analyze the DNA origami and DNA-based nanostructures as a drug delivery system. Besides their physical-chemical nature, we dissect the critical factors such as sta...

  7. A Pseudo DNA Cryptography Method

    OpenAIRE

    Ning, Kang

    2009-01-01

    The DNA cryptography is a new and very promising direction in cryptography research. DNA can be used in cryptography for storing and transmitting the information, as well as for computation. Although in its primitive stage, DNA cryptography is shown to be very effective. Currently, several DNA computing algorithms are proposed for quite some cryptography, cryptanalysis and steganography problems, and they are very powerful in these areas. However, the use of the DNA as a means of cryptography...

  8. Forensic DNA Profiling and Database

    OpenAIRE

    Panneerchelvam, S.; Norazmi, M.N.

    2003-01-01

    The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection.

  9. Local chromatin microenvironment determines DNMT activity : from DNA methyltransferase to DNA demethylase or DNA dehydroxymethylase

    NARCIS (Netherlands)

    van der Wijst, Monique G. P.; Venkiteswaran, Muralidhar; Chen, Hui; Xu, Guo-Liang; Plosch, Torsten; Rots, Marianne G.

    2015-01-01

    Insights on active DNA demethylation disproved the original assumption that DNA methylation is a stable epigenetic modification. Interestingly, mammalian DNA methyltransferases 3A and 3B (DNMT-3A and -3B) have also been reported to induce active DNA demethylation, in addition to their well-known fun

  10. Teacher-to-Teacher: An Annotated Bibliography on DNA and Genetic Engineering.

    Science.gov (United States)

    Mertens, Thomas R., Comp.

    1984-01-01

    Presented is an annotated bibliography of 24 books on DNA and genetic engineering. Areas considered in these books include: basic biological concepts to help understand advances in genetic engineering; applications of genetic engineering; social, legal, and moral issues of genetic engineering; and historical aspects leading to advances in…

  11. DNA and RNA analysis of blood and muscle from bodies with variable postmortem intervals

    DEFF Research Database (Denmark)

    Hansen, Jakob; Lesnikova, Iana; Funder, Anette Mariane Daa;

    2014-01-01

    formalin fixed and paraffin embedded (FFPE) muscle specimens. A quality assessment of muscle-derived DNA showed increased fragmentation with advancing body decomposition and generally more fragmentation in DNA from FFPE tissue than in DNA from frozen tissue. It was possible to amplify 1,000 basepair (bp......) DNA fragments from all samples with postmortem intervals below 3 days whereas 400-600 bp long fragments typically could be amplified from the most decomposed muscle specimens. RNA was less stable than DNA in postmortem muscle tissue, yet selected mRNA molecules could be detected by reverse......-transcriptase PCR in all samples up to 3 days after death. We conclude that analysis of DNA from bodies with a wide postmortem interval range is usually possible whereas the consistency of RNA analyses decreases considerably 3 days postmortem. We showed that muscle tissue is a highly usable source of DNA and RNA...

  12. A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA

    CERN Document Server

    Fosado, Y A G; Allan, J; Brackley, C; Henrich, O; Marenduzzo, D

    2016-01-01

    The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide level which retains the characteristic helical structure, while being able to simulate large molecules -- up to a million base pairs -- for time-scales which are relevant to physiological processes. This is made possible by an efficient and highly-parallelised implementation of the model which we discuss here. We compare the behaviour of our model with single molecule experiments where dsDNA is manipulated by external forces or torques. We also present some results on the kinetics of denaturation of linear DNA.

  13. Regulating the Transport of DNA through Biofriendly Nanochannels in a Thin Solid Membrane

    Science.gov (United States)

    Wang, Deqiang; Harrer, Stefan; Luan, Binquan; Stolovitzky, Gustavo; Peng, Hongbo; Afzali-Ardakani, Ali

    2014-02-01

    Channels formed by membrane proteins regulate the transport of water, ions or nutrients that are essential to cells' metabolism. Recent advances in nanotechnology allow us to fabricate solid-state nanopores for transporting and analyzing biomolecules. However, uncontrollable surface properties of a fabricated nanopore cause irregular transport of biomolecules, limiting potential biomimetic applications. Here we show that a nanopore functionalized with a self-assembled monolayer (SAM) can potentially regulate the transport of a DNA molecule by changing functional groups of the SAM. We found that an enhanced interaction between DNA and a SAM-coated nanopore can slow down the translocation speed of DNA molecules and increase the DNA capture-rate. Our results demonstrate that the transport of DNA molecules inside nanopores could be modulated by coating a SAM on the pore surface. Our method to control the DNA motion inside a nanopore may find its applications in nanopore-based DNA sequencing devices.

  14. Human DNA polymerase α in binary complex with a DNA:DNA template-primer

    OpenAIRE

    Javier Coloma; Johnson, Robert E.; Louise Prakash; Satya Prakash; Aggarwal, Aneel K.

    2016-01-01

    The Polα/primase complex assembles the short RNA-DNA fragments for priming of lagging and leading strand DNA replication in eukaryotes. As such, the Polα polymerase subunit encounters two types of substrates during primer synthesis: an RNA:DNA helix and a DNA:DNA helix. The engagement of the polymerase subunit with the DNA:DNA helix has been suggested as the of basis for primer termination in eukaryotes. However, there is no structural information on how the Polα polymerase subunit actually e...

  15. Evidence for DNA Damage as a Biological Link Between Diabetes and Cancer

    Directory of Open Access Journals (Sweden)

    Shao Chin Lee

    2015-01-01

    Full Text Available Objective: This review examines the evidence that: Diabetes is a state of DNA damage; pathophysiological factors in diabetes can cause DNA damage; DNA damage can cause mutations; and DNA mutation is linked to carcinogenesis. Data Sources: We retrieved information from the PubMed database up to January, 2014, using various search terms and their combinations including DNA damage, diabetes, cancer, high glucose, hyperglycemia, free fatty acids, palmitic acid, advanced glycation end products, mutation and carcinogenesis. Study Selection: We included data from peer-reviewed journals and a textbook printed in English on relationships between DNA damage and diabetes as well as pathophysiological factors in diabetes. Publications on relationships among DNA damage, mutagenesis, and carcinogenesis, were also reviewed. We organized this information into a conceptual framework to explain the possible causal relationship between DNA damage and carcinogenesis in diabetes. Results: There are a large amount of data supporting the view that DNA mutation is a typical feature in carcinogenesis. Patients with type 2 diabetes have increased production of reactive oxygen species, reduced levels of antioxidant capacity, and increased levels of DNA damage. The pathophysiological factors and metabolic milieu in diabetes can cause DNA damage such as DNA strand break and base modification (i.e., oxidation. Emerging experimental data suggest that signal pathways (i.e., Akt/tuberin link diabetes to DNA damage. This collective evidence indicates that diabetes is a pathophysiological state of oxidative stress and DNA damage which can lead to various types of mutation to cause aberration in cells and thereby increased cancer risk. Conclusions: This review highlights the interrelationships amongst diabetes, DNA damage, DNA mutation and carcinogenesis, which suggests that DNA damage can be a biological link between diabetes and cancer.

  16. Evidence for DNA Damage as a Biological Link Between Diabetes and Cancer

    Science.gov (United States)

    Lee, Shao Chin; Chan, Juliana CN

    2015-01-01

    Objective: This review examines the evidence that: Diabetes is a state of DNA damage; pathophysiological factors in diabetes can cause DNA damage; DNA damage can cause mutations; and DNA mutation is linked to carcinogenesis. Data Sources: We retrieved information from the PubMed database up to January, 2014, using various search terms and their combinations including DNA damage, diabetes, cancer, high glucose, hyperglycemia, free fatty acids, palmitic acid, advanced glycation end products, mutation and carcinogenesis. Study Selection: We included data from peer-reviewed journals and a textbook printed in English on relationships between DNA damage and diabetes as well as pathophysiological factors in diabetes. Publications on relationships among DNA damage, mutagenesis, and carcinogenesis, were also reviewed. We organized this information into a conceptual framework to explain the possible causal relationship between DNA damage and carcinogenesis in diabetes. Results: There are a large amount of data supporting the view that DNA mutation is a typical feature in carcinogenesis. Patients with type 2 diabetes have increased production of reactive oxygen species, reduced levels of antioxidant capacity, and increased levels of DNA damage. The pathophysiological factors and metabolic milieu in diabetes can cause DNA damage such as DNA strand break and base modification (i.e., oxidation). Emerging experimental data suggest that signal pathways (i.e., Akt/tuberin) link diabetes to DNA damage. This collective evidence indicates that diabetes is a pathophysiological state of oxidative stress and DNA damage which can lead to various types of mutation to cause aberration in cells and thereby increased cancer risk. Conclusions: This review highlights the interrelationships amongst diabetes, DNA damage, DNA mutation and carcinogenesis, which suggests that DNA damage can be a biological link between diabetes and cancer. PMID:26021514

  17. Electroeluting DNA fragments.

    Science.gov (United States)

    Zarzosa-Alvarez, Ana L; Sandoval-Cabrera, Antonio; Torres-Huerta, Ana L; Bermudez-Cruz, Rosa M

    2010-01-01

    Purified DNA fragments are used for different purposes in Molecular Biology and they can be prepared by several procedures. Most of them require a previous electrophoresis of the DNA fragments in order to separate the band of interest. Then, this band is excised out from an agarose or acrylamide gel and purified by using either: binding and elution from glass or silica particles, DEAE-cellulose membranes, "crush and soak method", electroelution or very often expensive commercial purification kits. Thus, selecting a method will depend mostly of what is available in the laboratory. The electroelution procedure allows one to purify very clean DNA to be used in a large number of applications (sequencing, radiolabeling, enzymatic restriction, enzymatic modification, cloning etc). This procedure consists in placing DNA band-containing agarose or acrylamide slices into sample wells of the electroeluter, then applying current will make the DNA fragment to leave the agarose and thus be trapped in a cushion salt to be recovered later by ethanol precipitation. PMID:20834225

  18. Programmable Quantitative DNA Nanothermometers.

    Science.gov (United States)

    Gareau, David; Desrosiers, Arnaud; Vallée-Bélisle, Alexis

    2016-07-13

    Developing molecules, switches, probes or nanomaterials that are able to respond to specific temperature changes should prove of utility for several applications in nanotechnology. Here, we describe bioinspired strategies to design DNA thermoswitches with programmable linear response ranges that can provide either a precise ultrasensitive response over a desired, small temperature interval (±0.05 °C) or an extended linear response over a wide temperature range (e.g., from 25 to 90 °C). Using structural modifications or inexpensive DNA stabilizers, we show that we can tune the transition midpoints of DNA thermometers from 30 to 85 °C. Using multimeric switch architectures, we are able to create ultrasensitive thermometers that display large quantitative fluorescence gains within small temperature variation (e.g., > 700% over 10 °C). Using a combination of thermoswitches of different stabilities or a mix of stabilizers of various strengths, we can create extended thermometers that respond linearly up to 50 °C in temperature range. Here, we demonstrate the reversibility, robustness, and efficiency of these programmable DNA thermometers by monitoring temperature change inside individual wells during polymerase chain reactions. We discuss the potential applications of these programmable DNA thermoswitches in various nanotechnology fields including cell imaging, nanofluidics, nanomedecine, nanoelectronics, nanomaterial, and synthetic biology. PMID:27058370

  19. Structural insight into negative DNA supercoiling by DNA gyrase, a bacterial type 2A DNA topoisomerase

    OpenAIRE

    Papillon, Julie; Ménétret, Jean-François; Batisse, Claire; Hélye, Reynald; Schultz, Patrick; Potier, Noëlle; Lamour, Valérie

    2013-01-01

    Type 2A DNA topoisomerases (Topo2A) remodel DNA topology during replication, transcription and chromosome segregation. These multisubunit enzymes catalyze the transport of a double-stranded DNA through a transient break formed in another duplex. The bacterial DNA gyrase, a target for broad-spectrum antibiotics, is the sole Topo2A enzyme able to introduce negative supercoils. We reveal here for the first time the architecture of the full-length Thermus thermophilus DNA gyrase alone and in a cl...

  20. Synapsis of DNA ends by DNA-dependent protein kinase

    OpenAIRE

    DeFazio, Lisa G.; Stansel, Rachel M.; Griffith, Jack D.; Chu, Gilbert

    2002-01-01

    The catalytic subunit of DNA-dependent protein kinase (DNA-PKCS) is required for a non-homologous end-joining pathway that repairs DNA double-strand breaks produced by ionizing radiation or V(D)J recombination; however, its role in this pathway has remained obscure. Using a neutravidin pull-down assay, we found that DNA-PKCS mediates formation of a synaptic complex containing two DNA molecules. Furthermore, kinase activity was cooperative with respect to DNA concentration, suggesting that act...

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

    Directory of Open Access Journals (Sweden)

    David R Halpin

    2004-07-01

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

  2. DNA repair and DNA antibodies during experimental mycoplasma arthritis

    International Nuclear Information System (INIS)

    To clarify the pathogenesis of a mycoplasma induced arthritis in rats, investigations were carried out on the influence of mycoplasma infection on DNA repair and the occurrence of DNA antibodies. During acute and subacute stage of the experimentally induced arthritis an inhibition of DNA repair could be observed. Besides the results indicated a correlation between reduced or inhibited DNA repair and the appearance of DNA antibodies could be found. The DNA-repair behaviour after the mycoplasma infection was compared with the influence of γ-irradiation

  3. DNA-mediated charge transport for DNA repair

    OpenAIRE

    Boon, Elizabeth M; Livingston, Alison L.; Chmiel, Nikolas H.; David, Sheila S.; Barton, Jacqueline K.

    2003-01-01

    MutY, like many DNA base excision repair enzymes, contains a [4Fe4S](2+) cluster of undetermined function. Electrochemical studies of MutY bound to a DNA-modified gold electrode demonstrate that the [4Fe4S] cluster of MutY can be accessed in a DNA-mediated redox reaction. Although not detectable without DNA, the redox potential of DNA-bound MutY is approximate to275 mV versus NHE, which is characteristic of HiPiP iron proteins. Binding to DNA is thus associated with a change in [4Fe4S](3+/2+)...

  4. [DNA methylation in obesity].

    Science.gov (United States)

    Pokrywka, Małgorzata; Kieć-Wilk, Beata; Polus, Anna; Wybrańska, Iwona

    2014-01-01

    The number of overweight and obese people is increasing at an alarming rate, especially in the developed and developing countries. Obesity is a major risk factor for diabetes, cardiovascular disease, and cancer, and in consequence for premature death. The development of obesity results from the interplay of both genetic and environmental factors, which include sedentary life style and abnormal eating habits. In the past few years a number of events accompanying obesity, affecting expression of genes which are not directly connected with the DNA base sequence (e.g. epigenetic changes), have been described. Epigenetic processes include DNA methylation, histone modifications such as acetylation, methylation, phosphorylation, ubiquitination, and sumoylation, as well as non-coding micro-RNA (miRNA) synthesis. In this review, the known changes in the profile of DNA methylation as a factor affecting obesity and its complications are described. PMID:25531701

  5. DNA sequencing: chemical methods

    International Nuclear Information System (INIS)

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

  6. DNA Topoisomerases in Transcription

    DEFF Research Database (Denmark)

    Rødgaard, Morten Terpager

    2015-01-01

    This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most of the ex......This Ph.D. thesis summarizes the main results of my studies on the interplay between DNA topoisomerases and transcription. The work was performed from 2011 to 2015 at Aarhus University in the Laboratory of Genome Research, and was supervised by associate professor Anni H. Andersen. Most...... topoisomerase-DNA cleavage complex. The second study is an investigation of how topoisomerases influence gene regulation by keeping the genome in an optimal topological state....

  7. Tunnelling microscopy of DNA

    Science.gov (United States)

    Selci, Stefano; Cricenti, Antonio

    1991-01-01

    Uncoated DNA molecules marked with an activated tris (1-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with a high resolution Scanning Tunnelling Microscope (STM). The STM operated simultaneously in the constant-current and gap-modulated mode. Highly reproducible STM images have been obtained and interpreted in terms of expected DNA structure. The main periodicity, regularly presented in molecules several hundred Ångstrom long, ranges from 25 Å to 35 Å with an average diameter of 22 Å. Higher resolution images of the minor groove have revealed the phosphate groups along the DNA backbones. Constant-current images of TAPO deposited on gold show a crystalline structure of rows of molecules with a side-by-side spacing of 3 Å.

  8. Highly Effective DNA Extraction Method from Fresh, Frozen, Dried and Clotted Blood Samples

    Directory of Open Access Journals (Sweden)

    Jaleh Barar

    2011-09-01

    Full Text Available Introduction: Today, with the tremendous potential of genomics and other recent advances in science, the role of science to improve reliable DNA extraction methods is more relevant than ever before. The ideal process for genomic DNA extraction demands high quantities of pure, integral and intact genomic DNA (gDNA from the sample with minimal co-extraction of inhibitors of downstream processes. Here, we report the development of a very rapid, less-hazardous, and high throughput protocol for extracting of high quality DNA from blood samples. Methods: Dried, clotted and ethylene diamine tetra-acetic acid (EDTA treated fresh and frozen blood samples were extracted using this method in which the quality and integrity of the extracted DNA were corroborated by agarose gel electrophoresis, PCR reaction and DNA digestion using restricted enzyme. The UV spectrophotometric and gel electrophoresis analysis resulted in high A260/A280 ratio (>1.8 with high intactness of DNA. Results: PCR and DNA digestion experiments indicated that the final solutions of extracted DNA contained no inhibitory substances, which confirms that the isolated DNA is of good quality. Conclusion: The high quality and quantity of current method, no enzymatic processing and accordingly its low cost, make it appropriate for DNA extraction not only from human but also from animal blood samples in any molecular biology labs.

  9. Developing strategies to increase plasmid DNA production in Escherichia coli DH5α using batch culture.

    Science.gov (United States)

    Islas-Lugo, Fabiola; Vega-Estrada, Jesús; Alvis, Christian Ariel; Ortega-López, Jaime; Del Carmen Montes-Horcasitas, María

    2016-09-10

    Plasmid DNA (pDNA) production has recently increased as a result of advances in DNA vaccines. The practical development of pDNA vaccines requires high yield and productivity of supercoiled plasmid DNA (sc-pDNA). The yield and productivity are influenced by the host strain, the plasmid, the production process, and especially by growth conditions, such as the culture type and medium. We evaluated different strategies to increase pDNA production by Escherichia coli DH5α in batch culture. The strategies were driven by the development of a four single-factor experimental design and were based on the change of culture media composition in terms of carbon and nitrogen and the modification of the pH control by using NaOH or NH4OH. The results revealed the carbon (50g/L of glycerol) and nitrogen (8.34g/L of YESP) concentration in the culture medium and starting pH control with NH4OH when most of the organic nitrogen was consumed. Under these conditions, we obtained a volumetric yield of 213mg pDNA/L, a specific yield of 10mg pDNA/g DCW (dry cell weight), 92% of sc-pDNA and a productivity of 17.6mg pDNA/(Lh). The pDNA productivities reached were 42% higher than the productivities reported by other authors applying similar conditions. PMID:27374404

  10. DNA damage checkpoint recovery and cancer development

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Haiyong [First affiliated hospital, Zhejiang University, School of medicine, Cancer Center, 79 Qingchun Road, Hangzhou 310003 (China); Zhang, Xiaoshan [Department of Genetics, University of Texas M.D. Anderson Cancer Center, Department of Genetics Unit 1010, 1515 Holcombe Blvd. Houston, TX 77030 (United States); Teng, Lisong, E-mail: lsteng@zju.edu.cn [First affiliated hospital, Zhejiang University, School of medicine, Cancer Center, 79 Qingchun Road, Hangzhou 310003 (China); Legerski, Randy J., E-mail: rlegersk@mdanderson.org [Department of Genetics, University of Texas M.D. Anderson Cancer Center, Department of Genetics Unit 1010, 1515 Holcombe Blvd. Houston, TX 77030 (United States)

    2015-06-10

    Cell cycle checkpoints were initially presumed to function as a regulator of cell cycle machinery in response to different genotoxic stresses, and later found to play an important role in the process of tumorigenesis by acting as a guard against DNA over-replication. As a counterpart of checkpoint activation, the checkpoint recovery machinery is working in opposition, aiming to reverse the checkpoint activation and resume the normal cell cycle. The DNA damage response (DDR) and oncogene induced senescence (OIS) are frequently found in precancerous lesions, and believed to constitute a barrier to tumorigenesis, however, the DDR and OIS have been observed to be diminished in advanced cancers of most tissue origins. These findings suggest that when progressing from pre-neoplastic lesions to cancer, DNA damage checkpoint barriers are overridden. How the DDR checkpoint is bypassed in this process remains largely unknown. Activated cytokine and growth factor-signaling pathways were very recently shown to suppress the DDR and to promote uncontrolled cell proliferation in the context of oncovirus infection. In recent decades, data from cell line and tumor models showed that a group of checkpoint recovery proteins function in promoting tumor progression; data from patient samples also showed overexpression of checkpoint recovery proteins in human cancer tissues and a correlation with patients' poor prognosis. In this review, the known cell cycle checkpoint recovery proteins and their roles in DNA damage checkpoint recovery are reviewed, as well as their implications in cancer development. This review also provides insight into the mechanism by which the DDR suppresses oncogene-driven tumorigenesis and tumor progression. - Highlights: • DNA damage checkpoint works as a barrier to cancer initiation. • DDR machinary response to genotoxic and oncogenic stress in similar way. • Checkpoint recovery pathways provide active signaling in cell cycle control. • Checkpoint

  11. DNA damage checkpoint recovery and cancer development

    International Nuclear Information System (INIS)

    Cell cycle checkpoints were initially presumed to function as a regulator of cell cycle machinery in response to different genotoxic stresses, and later found to play an important role in the process of tumorigenesis by acting as a guard against DNA over-replication. As a counterpart of checkpoint activation, the checkpoint recovery machinery is working in opposition, aiming to reverse the checkpoint activation and resume the normal cell cycle. The DNA damage response (DDR) and oncogene induced senescence (OIS) are frequently found in precancerous lesions, and believed to constitute a barrier to tumorigenesis, however, the DDR and OIS have been observed to be diminished in advanced cancers of most tissue origins. These findings suggest that when progressing from pre-neoplastic lesions to cancer, DNA damage checkpoint barriers are overridden. How the DDR checkpoint is bypassed in this process remains largely unknown. Activated cytokine and growth factor-signaling pathways were very recently shown to suppress the DDR and to promote uncontrolled cell proliferation in the context of oncovirus infection. In recent decades, data from cell line and tumor models showed that a group of checkpoint recovery proteins function in promoting tumor progression; data from patient samples also showed overexpression of checkpoint recovery proteins in human cancer tissues and a correlation with patients' poor prognosis. In this review, the known cell cycle checkpoint recovery proteins and their roles in DNA damage checkpoint recovery are reviewed, as well as their implications in cancer development. This review also provides insight into the mechanism by which the DDR suppresses oncogene-driven tumorigenesis and tumor progression. - Highlights: • DNA damage checkpoint works as a barrier to cancer initiation. • DDR machinary response to genotoxic and oncogenic stress in similar way. • Checkpoint recovery pathways provide active signaling in cell cycle control. • Checkpoint

  12. Rigidity of melting DNA

    Science.gov (United States)

    Pal, Tanmoy; Bhattacharjee, Somendra M.

    2016-05-01

    The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in the other the double-stranded DNA is taken to have an intrinsic rigidity for bending. In both cases single strands are completely flexible. The change in the elastic constant for the flexible case due to thermally generated bubbles is obtained exactly. For the case of intrinsic rigidity, the elastic constant is found to be proportional to the square root of the bubble number fluctuation.

  13. DNA sensing unchained

    OpenAIRE

    Ablasser, Andrea; Hornung, Veit

    2013-01-01

    In two recent reports in Science, James Chen and colleagues provide compelling evidence that detection of cytosolic DNA triggers the production of a novel second messenger, cyclic GMP-AMP (cGAMP), which in turn activates a signaling pathway that induces type I interferons (IFNs) in a STING-dependent manner. They further unravel a key role for a so far uncharacterized murine protein E330016A19 (human homolog: C6ORF150), now termed cGAMP synthetase (cGAS), to act as the DNA sensor that generate...

  14. DNA banking and DNA databanking by academic and commercial laboratories

    Energy Technology Data Exchange (ETDEWEB)

    McEwen, J.E. [Eunice Kennedy Shriver Center, Waltham, MA (United States)]|[Boston College Law School, Newton, MA (United States); Reilly, P.R. [Eunice Kennedy Shriver Center, Waltham, MA (United States)

    1994-09-01

    The advent of DNA-based testing is giving rise to DNA banking (the long-term storage of cells, transformed cell lines, or extracted DNA for subsequent retrieval and analysis) and DNA data banking (the indefinite storage of information derived from DNA analysis). Large scale acquisition and storage of DNA and DNA data has important implications for the privacy rights of individuals. A survey of 148 academically based and commercial DNA diagnostic laboratories was conducted to determine: (1) the extent of their DNA banking activities; (2) their policies and experiences regarding access to DNA samples and data; (3) the quality assurance measures they employ; and (4) whether they have written policies and/or depositor`s agreements addressing specific issues. These issues include: (1) who may have access to DNA samples and data; (2) whether scientists may have access to anonymous samples or data for research use; (3) whether they have plans to contact depositors or retest samples if improved tests for a disorder become available; (4) disposition of samples at the end of the contract period if the laboratory ceases operations, if storage fees are unpaid, or after a death or divorce; (5) the consequence of unauthorized release, loss, or accidental destruction of samples; and (6) whether depositors may share in profits from the commercialization of tests or treatments developed in part from studies of stored DNA. The results suggest that many laboratories are banking DNA, that many have already amassed a large number of samples, and that a significant number plan to further develop DNA banking as a laboratory service over the next two years. Few laboratories have developed written policies governing DNA banking, and fewer still have drafted documents that define the rights and obligations of the parties. There may be a need for increased regulation of DNA banking and DNA data banking and for better defined policies with respect to protecting individual privacy.

  15. Advances in Applied Mechanics

    OpenAIRE

    2014-01-01

    Advances in Applied Mechanics draws together recent significant advances in various topics in applied mechanics. Published since 1948, Advances in Applied Mechanics aims to provide authoritative review articles on topics in the mechanical sciences, primarily of interest to scientists and engineers working in the various branches of mechanics, but also of interest to the many who use the results of investigations in mechanics in various application areas, such as aerospace, chemical, civil, en...

  16. Editorial: Advanced learning technologies

    OpenAIRE

    Yu-Ju Lan; Gang-Shan Fu; Stephen J.H. Yang; Jeff J.S. Huang

    2012-01-01

    Recent rapid development of advanced information technology brings high expectations of its potential to improvement and innovations in learning. This special issue is devoted to using some of the emerging technologies issues related to the topic of education and knowledge sharing, involving several cutting edge research outcomes from recent advancement of learning technologies. Advanced learning technologies are the composition of various related technologies and concepts such as mobile tech...

  17. Advances in Biological Science.

    Science.gov (United States)

    Oppenheimer, Steven B.; And Others

    1988-01-01

    Reviews major developments in areas that are at the cutting edge of biological research. Areas include: human anti-cancer gene, recombinant DNA techniques for the detection of Huntington disease carriers, and marine biology. (CW)

  18. Advancement of Molecular Morphology

    Institute of Scientific and Technical Information of China (English)

    顾江

    2004-01-01

    @@ Molecular morphology is a new discipline of medical science that studies morphology at the molecular level. This includes the investigation of occurrence and distribution of proteins, peptides, DNA and RNA sequences at the tissue, cellular, and ultrastructural levels.

  19. THE EXPRESSION OF DNA REPAIR GENE XPA IN ADVANCED NON-SMALL CELL LUNG CANCER AND ITS CLINICAL SIGNIFICANCE%DNA修复基因XPA在非小细胞肺癌中的表达及其临床意义

    Institute of Scientific and Technical Information of China (English)

    覃芳卉; 刘志辉; 谢伟敏; 廖小莉; 姚铠涛; 王洪学; 房亮; 陆永奎; 周文献; 胡晓桦

    2012-01-01

    目的:分析非小细胞肺癌(NSCLC)组织中DNA修复基因Xeroderma Pigmentosum Group A(XPA)的表达状况及其与临床病理特征的关系.方法:采用免疫组织化学方法(IHC)检测初治中晚期NSCLC患者癌组织中XPA的表达状况,采用χ2检验比较各亚组之间的XPA表达状况的差异.结果:109例NSCLC组织中XPA的阳性表达率为55.0%(60/109),其表达与性别、吸烟史有密切关系,在男性组中的阳性率(61.0%)显著高于女性组(37.0%)(P=0.030);吸烟组的XPA阳性率显著高于不吸烟组(分别为68.1%和45.2%,P=0.017);但在吸烟人群中,吸烟量不同的亚组间XPA的表达率未见明显差异.XPA阳性率在不同年龄、临床TNM分期、组织学类型或分化程度、淋巴结转移和远处转移亚组中的差异均无统计学意义(均P>0.05).结论:XPA在NSCLC组织中的表达状况与性别、吸烟状况密切相关,并可能与NSCLC的发生有关.%Objective: To investigate the association between the expression of DNA repair gene XPA with the clinicopathology characteristics in patients with advanced non-small cell lung cancer (NSCLC) and its clinical significance. Methods: The expression of XPA -was examined -with immunohistochemistry (IHC) , the positive expression rate of XPA in different clinicopathology characteristic groups -was analyzed. Re-sultS: In 109 patients with NSCLC, the positive rate of XPA was 55. 0% (60/109) , and the expression rate in males was significantly higher than that in females (61. 0% vs. 37. 0%, P = 0. 030). The expression rate -was also higher in smokers than in non-smokers (68. 1 % vs. 45. 2% , P =0. 017). There -were no significant differences in the expression of XPA among different ages, TNM stages, and pathological classification ( P >0. 05 for all). Conclusion: In NSCLC cases, the expression status of XPA is markedly associated with gender and smoking status. Thus, XPA may play a potential role in non-small cell lung cancer occur process.

  20. Mitochondrial DNA disease—molecular insights and potential routes to a cure

    Energy Technology Data Exchange (ETDEWEB)

    Russell, Oliver; Turnbull, Doug, E-mail: doug.turnbull@newcastle.ac.uk

    2014-07-01

    Mitochondrial DNA diseases are common neurological conditions caused by mutations in the mitochondrial genome or nuclear genes responsible for its maintenance. Current treatments for these disorders are focussed on the management of the symptoms, rather than the correction of biochemical defects caused by the mutation. This review focuses on the molecular effects of mutations, the symptoms they cause and current work focusing on the development of targeted treatments for mitochondrial DNA disease. - Highlights: • We discuss several common disease causing mtDNA mutations. • We highlight recent work linking pathogenicity to deletion size and heteroplasmy. • We discuss recent advances in the development of targeted mtDNA disease treatments.

  1. Imparting the unique properties of DNA into complex material architectures and functions

    Directory of Open Access Journals (Sweden)

    Phyllis F. Xu

    2013-07-01

    Full Text Available While the remarkable chemical and biological properties of DNA have been known for decades, these properties have only been imparted into materials with unprecedented function much more recently. The inimitable ability of DNA to form programmable, complex assemblies through stable, specific, and reversible molecular recognition has allowed the creation of new materials through DNA's ability to control a material's architecture and properties. In this review we discuss recent progress in how DNA has brought unmatched function to materials, focusing specifically on new advances in delivery agents, devices, and sensors.

  2. Timing, coordination, and rhythm: Acrobatics at the DNA replication fork

    KAUST Repository

    Hamdan, Samir

    2010-04-09

    In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In several prokaryotic systems studied so far, this problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. The timing of Okazaki fragment synthesis and loop formation is determined by a subtle interplay of enzymatic activities at the fork. Recent developments in single-molecule techniques have enabled the direct observation of these processes and have greatly contributed to a better understanding of the dynamic nature of the replication fork. Here, we will review recent experimental advances, present the current models, and discuss some of the exciting developments in the field. 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Plant DNA barcoding in China

    Institute of Scientific and Technical Information of China (English)

    De-Zhu LI; Jian-Quan LIU; Zhi-Duan CHEN; Hong WANG; Xue-Jun GE; Shi-Liang ZHOU; Lian-Ming GAO; Cheng-Xin FU; Shi-Lin CHEN

    2011-01-01

    @@ Identification is the keystone of biology (Bell, 1986).However, to biologists and students of biology, the total numbers of species that must be identified far outnumber the names commonly used in English, Chinese, or other living languages.In addition, the identification cues vary greatly between different taxonomical groups.Even for the taxonomists with long training and experience, it is difficult to remember all specific terms for a given group, e.g., Orchidaceae or Poaceae, without help of floristic books or monographs.It takes much time and effort to train a taxonomist, at a time when fewer and fewer young students are interested in this "classical" and "out-of-style", but extremely important, discipline.Many students elect to learn the more "advanced'' and "modem" biological disciples like molecular biology and biochemistry.Thus, in China and therest of the world, taxonomists are themselves becoming "endangered".The rise of the DNA barcoding is expected to mitigate, at least in part, this dilemma.

  4. DNA ligase I selectively affects DNA synthesis by DNA polymerases delta and epsilon suggesting differential functions in DNA replication and repair.

    OpenAIRE

    Mossi, R; Ferrari, E.; Hübscher, U

    1998-01-01

    The joining of single-stranded breaks in double-stranded DNA is an essential step in many important processes such as DNA replication, DNA repair, and genetic recombination. Several data implicate a role for DNA ligase I in DNA replication, probably coordinated by the action of other enzymes and proteins. Since both DNA polymerases delta and epsilon show multiple functions in different DNA transactions, we investigated the effect of DNA ligase I on various DNA synthesis events catalyzed by th...

  5. DNA supercoiling and its role in DNA decatenation and unknotting

    OpenAIRE

    Witz, Guillaume; Stasiak, Andrzej

    2009-01-01

    Chromosomal and plasmid DNA molecules in bacterial cells are maintained under torsional tension and are therefore supercoiled. With the exception of extreme thermophiles, supercoiling has a negative sign, which means that the torsional tension diminishes the DNA helicity and facilitates strand separation. In consequence, negative supercoiling aids such processes as DNA replication or transcription that require global- or local-strand separation. In extreme thermophiles, DNA is positively supe...

  6. Slowing DNA Transport Using Graphene–DNA Interactions

    OpenAIRE

    Banerjee, Shouvik; Wilson, James; Shim, Jiwook; Shankla, Manish; Corbin, Elise A.; Aksimentiev, Aleksei; Bashir, Rashid

    2014-01-01

    Slowing down DNA translocation speed in a nanopore is essential to ensuring reliable resolution of individual bases. Thin membrane materials enhance spatial resolution but simultaneously reduce the temporal resolution as the molecules translocate far too quickly. In this study, the effect of exposed graphene layers on the transport dynamics of both single (ssDNA) and double-stranded DNA (dsDNA) through nanopores is examined. Nanopore devices with various combinations of graphene and Al2O3 die...

  7. cDNA: 12295 [

    Lifescience Database Archive (English)

    Full Text Available H. sapiens + Hs.267288 Homo sapiens full open reading ... frame cDNA clone RZPDo834G0212D for gene C ... 6orf55, chromosome 6 open reading ... frame 55; complete cds, incl. stopcodon gnl|UG|Hs# ...

  8. cDNA: 16610 [

    Lifescience Database Archive (English)

    Full Text Available H. sapiens + Hs.62595 Homo sapiens full open reading ... frame cDNA clone RZPDo834H088D for gene C9o ... rf9, chromosome 9 open reading ... frame 9; complete cds, incl. stopcodon gnl|UG|Hs#S ...

  9. TRANSFECTION WITH BACULOVIRUS DNA

    Science.gov (United States)

    Purified DNA from the nuclear polyhedrosis viruses of Autographa californica (AcM NPV) and Rachiplusia ou (RoM NPV) were found to be infectious in TN-368 cells employing the calcium phosphate precipitation technique (F.L. Graham and A.J. van der Eb, Virology, 52, 456-467, 1973). ...

  10. Field Deployable DNA analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Wheeler, E; Christian, A; Marion, J; Sorensen, K; Arroyo, E; Vrankovich, G; Hara, C; Nguyen, C

    2005-02-09

    This report details the feasibility of a field deployable DNA analyzer. Steps for swabbing cells from surfaces and extracting DNA in an automatable way are presented. Since enzymatic amplification reactions are highly sensitive to environmental contamination, sample preparation is a crucial step to make an autonomous deployable instrument. We perform sample clean up and concentration in a flow through packed bed. For small initial samples, whole genome amplification is performed in the packed bed resulting in enough product for subsequent PCR amplification. In addition to DNA, which can be used to identify a subject, protein is also left behind, the analysis of which can be used to determine exposure to certain substances, such as radionuclides. Our preparative step for DNA analysis left behind the protein complement as a waste stream; we determined to learn if the proteins themselves could be analyzed in a fieldable device. We successfully developed a two-step lateral flow assay for protein analysis and demonstrate a proof of principle assay.

  11. cDNA: 3940 [

    Lifescience Database Archive (English)

    Full Text Available H. sapiens - Hs.7188 Homo sapiens cDNA PSEC0078 fis, clone NT2RP2004036, moderately similar to M ... -Sema F=a factor in neural network ... development. gnl|UG|Hs#S4806431 AK075388 2/887_394 ...

  12. cDNA: 41587 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.30133 Mus musculus 18-day embryo whole body cDNA, RIKEN full-length enriched li ... brary, clone:1110004A14 product:ethanol ... induced 6, full insert sequence gnl|UG|Mm#S9085518 ...

  13. cDNA: 39377 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus + Mm.7091 Mus musculus adult pancreas islet cells cDNA, RIKEN fu ll-length enriched l ... R BETA SUBUNIT) (SSR-BETA) homolog [Homo sapiens], fu ... ... gnl|UG|Mm#S10839939 AK050505 3/6436_39377.png ...

  14. cDNA: 46817 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus + Mm.30092 Mus musculus adult male cerebellum cDNA, RIKEN fu ll-length enriched libra ... 1 PRECURSOR (EC 3.4.21.-) homolog [Homo sapiens], fu ... ... gnl|UG|Mm#S10838326 AK075719 8/7837_46817.png ...

  15. cDNA: 56670 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.10747 Mus musculus adult male testis cDNA, RIKEN fu ll-length enriched library, ... PONSE FACTOR) (MRF-1) homolog [Rattus norvegicus], fu ... ... gnl|UG|Mm#S9083407 AK006184 17/9809_56670.png ...

  16. cDNA: 56898 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.10747 Mus musculus adult male testis cDNA, RIKEN fu ll-length enriched library, ... PONSE FACTOR) (MRF-1) homolog [Rattus norvegicus], fu ... ... gnl|UG|Mm#S9083407 AK006184 17/9810_56898.png ...

  17. cDNA: 56671 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.10747 Mus musculus adult male testis cDNA, RIKEN fu ll-length enriched library, ... PONSE FACTOR) (MRF-1) homolog [Rattus norvegicus], fu ... ... gnl|UG|Mm#S9083172 AK006562 17/9809_56671.png ...

  18. cDNA: 56677 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.10747 Mus musculus adult male testis cDNA, RIKEN fu ll-length enriched library, ... PONSE FACTOR) (MRF-1) homolog [Rattus norvegicus], fu ... ... gnl|UG|Mm#S9083407 AK006184 17/9809_56677.png ...

  19. cDNA: 56899 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.10747 Mus musculus adult male testis cDNA, RIKEN fu ll-length enriched library, ... PONSE FACTOR) (MRF-1) homolog [Rattus norvegicus], fu ... ... gnl|UG|Mm#S9083172 AK006562 17/9810_56899.png ...

  20. cDNA: 46327 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus + Mm.292517 Mus musculus 12 days embryo spinal ganglion cDNA, RIKEN fu ll-length enri ... PHA CHAIN) (PHERS) (CML33) homolog [Homo sapiens], fu ... ... gnl|UG|Mm#S10835133 AK084031 8/7824_46327.png ...

  1. cDNA: 56891 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.10747 Mus musculus adult male testis cDNA, RIKEN fu ll-length enriched library, ... PONSE FACTOR) (MRF-1) homolog [Rattus norvegicus], fu ... ... gnl|UG|Mm#S9083407 AK006184 17/9810_56891.png ...

  2. cDNA: 56678 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.10747 Mus musculus adult male testis cDNA, RIKEN fu ll-length enriched library, ... PONSE FACTOR) (MRF-1) homolog [Rattus norvegicus], fu ... ... gnl|UG|Mm#S9083172 AK006562 17/9809_56678.png ...

  3. cDNA: 41699 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus + Mm.246636 Mus musculus adult male testis cDNA, RIKEN fu ll-length enriched library, ... e/G-protein beta WD-40 repeats containing protein, fu ... ... gnl|UG|Mm#S9075317 AK016965 5/6970_41699.png ...

  4. cDNA: 56892 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.10747 Mus musculus adult male testis cDNA, RIKEN fu ll-length enriched library, ... PONSE FACTOR) (MRF-1) homolog [Rattus norvegicus], fu ... ... gnl|UG|Mm#S9083172 AK006562 17/9810_56892.png ...

  5. cDNA: 36690 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus + Mm.345070 Mus musculus 16 days embryo head cDNA, RIKEN fu ll-length enriched librar ... SPLICEOSOME ASSOCIATED PROTEIN 49) [Homo sapiens], fu ... ... gnl|UG|Mm#S10835972 AK081584 2/6005_36690.png ...

  6. cDNA: 49729 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.286963 Mus musculus 10 days lactation, adult female mammary gland cDNA, RIKEN f ... d library, clone:D730027I09 product:similar to LAK-4P ... [Homo sapiens], full insert sequence gnl|UG|Mm#S10 ...

  7. cDNA: 40377 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.154312 Mus musculus 0 day neonate kidney cDNA, RIKEN full-length enriched libra ... ry, clone:D630023P19 product:HYPERTENSION ... RELATED PROTEIN 1, full insert sequence gnl|UG|Mm# ...

  8. cDNA: 45098 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus + Mm.334199 Mus musculus adult male aorta and vein cDNA, RIKEN full-length enriched ... library, clone:A530074J19 product:SA rat hypertension -associated homolog, full insert sequence gnl|UG|Mm ...

  9. cDNA: 40378 [

    Lifescience Database Archive (English)

    Full Text Available M. musculus - Mm.154312 Mus musculus 7 days embryo whole body cDNA, RIKEN full-length enriched l ... ibrary, clone:C430046A10 product:HYPERTENSION ... RELATED PROTEIN 1, full insert sequence gnl|UG|Mm# ...

  10. DNA tagged microparticles

    Energy Technology Data Exchange (ETDEWEB)

    Farquar, George R.; Leif, Roald N.; Wheeler, Elizabeth

    2016-03-22

    In one embodiment, a product includes a plurality of particles, each particle including: a carrier that includes a non-toxic material; and at least one DNA barcode coupled to the carrier, where the particles each have a diameter in a range from about 1 nanometer to about 100 microns.

  11. cDNA: 9471 [

    Lifescience Database Archive (English)

    Full Text Available H. sapiens + Hs.288986 Homo sapiens putative open reading frame; duplicate of the functional spi ... DNA clone BCD514, GenBank Accession Number U18423; it ... is not known if this copy of the gene is actually ...

  12. Borrowing Nuclear DNA Helicases to Protect Mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Lin Ding

    2015-05-01

    Full Text Available In normal cells, mitochondria are the primary organelles that generate energy, which is critical for cellular metabolism. Mitochondrial dysfunction, caused by mitochondrial DNA (mtDNA mutations or an abnormal mtDNA copy number, is linked to a range of human diseases, including Alzheimer’s disease, premature aging‎ and cancer. mtDNA resides in the mitochondrial lumen, and its duplication requires the mtDNA replicative helicase, Twinkle. In addition to Twinkle, many DNA helicases, which are encoded by the nuclear genome and are crucial for nuclear genome integrity, are transported into the mitochondrion to also function in mtDNA replication and repair. To date, these helicases include RecQ-like helicase 4 (RECQ4, petite integration frequency 1 (PIF1, DNA replication helicase/nuclease 2 (DNA2 and suppressor of var1 3-like protein 1 (SUV3. Although the nuclear functions of some of these DNA helicases have been extensively studied, the regulation of their mitochondrial transport and the mechanisms by which they contribute to mtDNA synthesis and maintenance remain largely unknown. In this review, we attempt to summarize recent research progress on the role of mammalian DNA helicases in mitochondrial genome maintenance and the effects on mitochondria-associated diseases.

  13. Lipophilic DNA-conjugates: DNA controlled assembly of liposomes

    DEFF Research Database (Denmark)

    Vogel, Stefan; Jakobsen, Ulla

    2009-01-01

    DNA detection systems based on encoded solid particles have been reported but require often tedious and not generally applicable surface chemistry. In the present study a system comprised of a lipid-modified DNA probe sequence and unmodified DNA target sequences is used to non-covalently assemble...

  14. Emerging roles of DNA-PK besides DNA repair.

    Science.gov (United States)

    Kong, Xianming; Shen, Ying; Jiang, Na; Fei, Xin; Mi, Jun

    2011-08-01

    The DNA-dependent protein kinase (DNA-PK) is a DNA-activated serine/threonine protein kinase, and abundantly expressed in almost all mammalian cells. The roles of DNA-PK in DNA-damage repair pathways, including non-homologous end-joining (NHEJ) repair and homologous recombinant (HR) repair, have been studied intensively. However, the high levels of DNA-PK in human cells are somewhat paradoxical in that it does not impart any increased ability to repair DNA damage. If DNA-PK essentially exceeds the demand for DNA damage repair, why do human cells universally express such high levels of this huge complex? DNA-PK has been recently reported to be involved in metabolic gene regulation in response to feeding/insulin stimulation; our studies have also suggested a role of DNA-PK in the regulation of the homeostasis of cell proliferation. These novel findings expand our horizons about the importance of DNA-PK. PMID:21514376

  15. Thermodynamic comparison of PNA/DNA and DNA/DNA hybridization reactions at ambient temperature.

    OpenAIRE

    Schwarz, F. P.; Robinson, S; Butler, J. M.

    1999-01-01

    The thermodynamics of 13 hybridization reactions between 10 base DNA sequences of design 5'-ATGCXYATGC-3' with X, Y = A, C, G, T and their complementary PNA and DNA sequences were determined from isothermal titration calorimetry (ITC) measurements at ambient temperature. For the PNA/DNA hybridization reactions, the binding constants range from 1.8 x 10(6)M(-1)for PNA(TT)/DNA to 4.15 x 10(7)M(-1)for PNA(GA)/DNA and the binding enthalpies range from -194 kJ mol(-1)for PNA(CG)/DNA to -77 kJ mol(...

  16. DNA polymerase beta can substitute for DNA polymerase I in the initiation of plasmid DNA replication.

    OpenAIRE

    Sweasy, J B; Chen, M.; Loeb, L A

    1995-01-01

    We previously demonstrated that mammalian DNA polymerase beta can substitute for DNA polymerase I of Escherichia coli in DNA replication and in base excision repair. We have now obtained genetic evidence suggesting that DNA polymerase beta can substitute for E. coli DNA polymerase I in the initiation of replication of a plasmid containing a pMB1 origin of DNA replication. Specifically, we demonstrate that a plasmid with a pMB1 origin of replication can be maintained in an E. coli polA mutant ...

  17. An Introduction to DNA Fingerprinting.

    Science.gov (United States)

    Hepfer, Carol Ely; And Others

    1993-01-01

    Provides background information on DNA fingerprinting, and describes exercises for introducing general biology students at the high school or college level to the methodology and applications of DNA fingerprinting. (PR)

  18. Esitleti kakskeelset luulekogu "Luule DNA"

    Index Scriptorium Estoniae

    2007-01-01

    Magrelli, Valerio. Luule DNA = Il DNA della poesia / tõlkinud [ja saatesõna:] Maarja Kangro ja Kalju Kruusa. Tallinn : Koma, 2006. Sisaldab autori teksti. Esitlus 24. jaan. Kirjanike majas Tallinnas

  19. Advances in PHWR design

    International Nuclear Information System (INIS)

    Recent advances by AECL in improved performance, cost reduction and safety improvement of CANDU reactors are described. Topics include: computer-aided design tools, up-front licensing, site utilization, plant life management, construction techniques, plant control, safety-critical software, advanced fuels, human-machine interface, heat sinks, radiation protection, feedback to design, emergency core cooling and probabilistic safety assessment

  20. Advances in chemical physics

    CERN Document Server

    Rice, Stuart A

    2008-01-01

    This series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. This stand-alone special topics volume reports recent advances in electron-transfer research with significant, up-to-date chapters by internationally recognized researchers.

  1. Advanced Manufacturing Technologies

    Science.gov (United States)

    Fikes, John

    2016-01-01

    Advanced Manufacturing Technologies (AMT) is developing and maturing innovative and advanced manufacturing technologies that will enable more capable and lower-cost spacecraft, launch vehicles and infrastructure to enable exploration missions. The technologies will utilize cutting edge materials and emerging capabilities including metallic processes, additive manufacturing, composites, and digital manufacturing. The AMT project supports the National Manufacturing Initiative involving collaboration with other government agencies.

  2. Advanced uranium enrichment technologies

    International Nuclear Information System (INIS)

    The Advanced Gas Centrifuge and Atomic Vapor Laser Isotope Separation methods are described. The status and potential of the technologies are summarized, the programs outlined, and the economic incentives are noted. How the advanced technologies, once demonstrated, might be deployed so that SWV costs in the 1990s can be significantly reduced is described

  3. Interfacing DNA nanodevices with biology: challenges, solutions and perspectives

    Science.gov (United States)

    Vinther, Mathias; Kjems, Jørgen

    2016-08-01

    The cellular machinery performs millions of complex reactions with extreme precision at nanoscale. From studying these reactions, scientists have become inspired to build artificial nanosized molecular devices with programmed functions. One of the fundamental tools in designing and creating these nanodevices is molecular self-assembly. In nature, deoxyribonucleic acid (DNA) is inarguably one of the most remarkable self-assembling molecules. Governed by the Watson–Crick base-pairing rules, DNA assembles with a structural reliability and predictability based on sequence composition unlike any other complex biological polymer. This consistency has enabled rational design of hundreds of two- and three-dimensional shapes with a molecular precision and homogeneity not preceded by any other known technology at the nanometer scale. During the last two decades, DNA nanotechnology has undergone a rapid evolution pioneered by the work of Nadrian Seeman (Kallenbach et al 1983 Nature 205 829–31). Especially the introduction of the versatile DNA Origami technique by Rothemund (2006 Nature 440 297–302) led to an efflorescence of new DNA-based self-assembled nanostructures (Andersen et al 2009 Nature 459 73–6, Douglas et al 2009 Nature 459 414–8, Dietz et al 2009 Science 325 725–30, Han et al 2011 Science 332 342–6, Iinuma et al 2014 Science 344 65–9), and variations of this technique have contributed to an increasing repertoire of DNA nanostructures (Wei et al 2012 Nature 485 623–6, Ke et al 2012 Science 338 1177–83, Benson et al 2015 Nature 523 441–4, Zhang et al 2015 Nat. Nanotechnol. 10 779–84, Scheible et al 2015 Small 11 5200–5). These advances have naturally triggered the question: What can these DNA nanostructures be used for? One of the leading proposals of use for DNA nanotechnology has been in biology and biomedicine acting as a molecular ‘nanorobot’ or smart drug interacting with the cellular machinery. In this review, we will explore and

  4. Nanopore-based Fourth-generation DNA Sequencing Technology

    Institute of Scientific and Technical Information of China (English)

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

    2015-01-01

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

  5. The DNA methylome of human peripheral blood mononuclear cells

    DEFF Research Database (Denmark)

    Li, Yingrui; Zhu, Jingde; Tian, Geng;

    2010-01-01

    DNA methylation plays an important role in biological processes in human health and disease. Recent technological advances allow unbiased whole-genome DNA methylation (methylome) analysis to be carried out on human cells. Using whole-genome bisulfite sequencing at 24.7-fold coverage (12.3-fold per...... strand), we report a comprehensive (92.62%) methylome and analysis of the unique sequences in human peripheral blood mononuclear cells (PBMC) from the same Asian individual whose genome was deciphered in the YH project. PBMC constitute an important source for clinical blood tests world-wide. We found...

  6. Alterations of ultraviolet irradiated DNA

    International Nuclear Information System (INIS)

    Thymine dimers production has been studied in several DNA-3H irradiated at various wave lenght of U.V. Light. The influence of dimers on the hydrodynamic and optic properties, thermal structural stability and transformant capacity of DNA have been studied too. At last the recognition and excision of dimers by the DNA-UV-Endonuclease and DNA-Polimerase-I was also studied. (author)

  7. Event extraction for DNA methylation

    OpenAIRE

    Ohta Tomoko; Pyysalo Sampo; Miwa Makoto; Tsujii Jun’ichi

    2011-01-01

    Abstract Background We consider the task of automatically extracting DNA methylation events from the biomedical domain literature. DNA methylation is a key mechanism of epigenetic control of gene expression and implicated in many cancers, but there has been little study of automatic information extraction for DNA methylation. Results We present an annotation scheme for DNA methylation following the representation of the BioNLP shared task on event extraction, select a set of 200 abstracts inc...

  8. Supramolecular Polymers in DNA Nanotechnology

    OpenAIRE

    Vyborna, Yuliia; Vybornyi, Mykhailo; Häner, Robert

    2016-01-01

    Creation of biocompatible functional materials is an important task in supramolecular chemistry. In this contribution, we report on noncovalent synthesis of DNA-grafted supramolecular polymers (SPs). DNA-grafted SPs enable programmed arrangement of oligonucleotides in a regular, tightly packed one-dimensional array. Further interactions of DNA-grafted SPs with complementary DNA strands leads to the formation of networks through highly cooperative G-C blunt-end stacking interactions. The struc...

  9. Recoiling DNA Molecule: Simulation & Experiment

    OpenAIRE

    Neto, Jose Coelho; Dickman, Ronald; Mesquita, O. N.

    2002-01-01

    Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the persistence length of single DNA molecules can also be measured based on the recoil dynamics of these DNA-microsphere complexes if appropriate corrections are made to the friction coefficient of the microsphere in the vicinity of the substrate. Comparison between co...

  10. Catalytic DNA with phosphatase activity

    OpenAIRE

    Chandrasekar, Jagadeeswaran; Silverman, Scott K.

    2013-01-01

    Catalytic DNA sequences (deoxyribozymes, DNA enzymes, or DNAzymes) have been identified by in vitro selection for various catalytic activities. Expanding the limits of DNA catalysis is an important fundamental objective and may facilitate practical utility of catalysts that can be obtained from entirely unbiased (random) sequence populations. In this study, we show that DNA can catalyze Zn2+-dependent phosphomonoester hydrolysis of tyrosine and serine side chains (i.e., exhibit phosphatase ac...

  11. Interpreting DNA Evidence: A Review

    OpenAIRE

    Foreman, L.A.; Champod, C.; Evett, I.W.; Lambert, J.A.; Pope, S.

    2003-01-01

    The paper provides a review of current issues relating to the use of DNA profiling in forensic science. A short historical section gives the main statistical milestones that occurred during a rapid development of DNA technology and operational uses. Greater detail is then provided for interpretation issues involving STR DNA profiles, including: ¶ methods that take account of population substructure in DNA calculations; ¶ parallel work carried out by the US National Research ...

  12. Forensic trace DNA: a review

    OpenAIRE

    van Oorschot Roland AH; Ballantyne Kaye N; Mitchell R John

    2010-01-01

    Abstract DNA analysis is frequently used to acquire information from biological material to aid enquiries associated with criminal offences, disaster victim identification and missing persons investigations. As the relevance and value of DNA profiling to forensic investigations has increased, so too has the desire to generate this information from smaller amounts of DNA. Trace DNA samples may be defined as any sample which falls below recommended thresholds at any stage of the analysis, from ...

  13. Dipole relaxation losses in DNA

    OpenAIRE

    Briman, M.; N. P. Armitage; Helgren, E.; Gruner, G.

    2003-01-01

    The electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the appreciable AC conductivity of DNA is not due to photon activated hopping between localized states, but instead due to dissipation from dipole motion in the surrounding water helix. Such a result, where the conductivity is due to the constrained motion of ove...

  14. Mechanisms for DNA Charge Transport

    OpenAIRE

    Genereux, Joseph C.; Barton, Jacqueline K.

    2010-01-01

    DNA charge transport (CT) chemistry has received considerable attention by scientific researchers over the past 15 years since our first provocative publication on long range CT in a DNA assembly.1,2 This interest, shared by physicists, chemists and biologists, reflects the potential of DNA CT to provide a sensitive route for signaling, whether in the construction of nanoscale biosensors or as an enzymatic tool to detect damage in the genome. Research into DNA CT chemistry began as a quest to...

  15. DNA-based hybrid catalysis

    NARCIS (Netherlands)

    Rioz-Martínez, Ana; Roelfes, Gerard

    2015-01-01

    In the past decade, DNA-based hybrid catalysis has merged as a promising novel approach to homogeneous (asymmetric) catalysis. A DNA hybrid catalysts comprises a transition metal complex that is covalently or supramolecularly bound to DNA. The chiral microenvironment and the second coordination sphe

  16. Environmental influences on DNA curvature

    DEFF Research Database (Denmark)

    Ussery, David; Higgins, C.F.; Bolshoy, A.

    1999-01-01

    DNA curvature plays an important role in many biological processes. To study environmentalinfluences on DNA curvature we compared the anomalous migration on polyacrylamide gels ofligation ladders of 11 specifically-designed oligonucleotides. At low temperatures (25 degreesC and below) most...... for DNAcurvature and for environmentally-sensitive DNA conformations in the regulation of geneexpression....

  17. DNA Sequential Logic Gate Using Two-Ring DNA.

    Science.gov (United States)

    Zhang, Cheng; Shen, Linjing; Liang, Chao; Dong, Yafei; Yang, Jing; Xu, Jin

    2016-04-13

    Sequential DNA detection is a fundamental issue for elucidating the interactive relationships among complex gene systems. Here, a sequential logic DNA gate was achieved by utilizing the two-ring DNA structure, with the ability to recognize "before" and "after" triggering sequences of DNA signals. By taking advantage of a "loop-open" mechanism, separations of two-ring DNAs were controlled. Three triggering pathways with different sequential DNA treatments were distinguished by comparing fluorescent outputs. Programmed nanoparticle arrangement guided by "interlocked" two-ring DNA was also constructed to demonstrate the achievement of designed nanostrucutres. Such sequential logic DNA operation may guide future molecular sensors to monitor more complex gene network in biological systems. PMID:26990044

  18. DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA

    DEFF Research Database (Denmark)

    Christensen, H.; Angen, Øystein; Mutters, R.; Olsen, J.E.; Bisgaard, M.

    2000-01-01

    The present study was aimed at reducing the time and labour used to perform DNA-DNA hybridizations for classification of bacteria at the species level. A micro-well-format DNA hybridization method was developed and validated. DNA extractions were performed by a small-scale method and DNA was...... sheared mechanically into fragments of between 400 and 700 bases. The hybridization conditions were calibrated according to DNA similarities obtained by the spectrophotometric method using strains within the family Pasteurellaceae, Optimal conditions were obtained with 300 ng DNA added per well and bound...... by covalent attachment to NucleoLink. Hybridization was performed with 500 ng DNA, 5% (w/w) of which was labelled with photo-activatable biotin (competitive hybridization) for 2.5 h at 65 degrees C in 2 x SSC followed by stringent washing with 2 x SSC at the same temperature. The criteria for...

  19. Genetics, structure, and prevalence of FP967 (CDC Triffid) T-DNA in flax.

    Science.gov (United States)

    Young, Lester; Hammerlindl, Joseph; Babic, Vivijan; McLeod, Jamille; Sharpe, Andrew; Matsalla, Chad; Bekkaoui, Faouzi; Marquess, Leigh; Booker, Helen M

    2015-01-01

    The detection of T-DNA from a genetically modified flaxseed line (FP967, formally CDC Triffid) in a shipment of Canadian flaxseed exported to Europe resulted in a large decrease in the amount of flax planted in Canada. The Canadian flaxseed industry undertook major changes to ensure the removal of FP967 from the supply chain. This study aimed to resolve the genetics and structure of the FP967 transfer DNA (T-DNA). The FP967 T-DNA is thought to be inserted in at single genomic locus. The junction between the T-DNA and genomic DNA consisted of two inverted Right Borders with no Left Border (LB) flanking genomic DNA sequences recovered. This information was used to develop an event-specific quantitative PCR (qPCR) assay. This assay and an existing assay specific to the T-DNA construct were used to determine the genetics and prevalence of the FP967 T-DNA. These data supported the hypothesis that the T-DNA is present at a single location in the genome. The FP967 T-DNA is present at a low level (between 0.01 and 0.1%) in breeder seed lots from 2009 and 2010. None of the 11,000 and 16,000 lines selected for advancement through the Flax Breeding Program in 2010 and 2011, respectively, tested positive for the FP967 T-DNA, however. Most of the FP967 T-DNA sequence was resolved via PCR cloning and next generation sequencing. A 3,720 bp duplication of an internal portion of the T-DNA (including a Right Border) was discovered between the flanking genomic DNA and the LB. An event-specific assay, SAT2-LB, was developed for the junction between this repeat and the LB. PMID:25883881

  20. Geant4-DNA simulations using complex DNA geometries generated by the DnaFabric tool

    Science.gov (United States)

    Meylan, S.; Vimont, U.; Incerti, S.; Clairand, I.; Villagrasa, C.

    2016-07-01

    Several DNA representations are used to study radio-induced complex DNA damages depending on the approach and the required level of granularity. Among all approaches, the mechanistic one requires the most resolved DNA models that can go down to atomistic DNA descriptions. The complexity of such DNA models make them hard to modify and adapt in order to take into account different biological conditions. The DnaFabric project was started to provide a tool to generate, visualise and modify such complex DNA models. In the current version of DnaFabric, the models can be exported to the Geant4 code to be used as targets in the Monte Carlo simulation. In this work, the project was used to generate two DNA fibre models corresponding to two DNA compaction levels representing the hetero and the euchromatin. The fibres were imported in a Geant4 application where computations were performed to estimate the influence of the DNA compaction on the amount of calculated DNA damage. The relative difference of the DNA damage computed in the two fibres for the same number of projectiles was found to be constant and equal to 1.3 for the considered primary particles (protons from 300 keV to 50 MeV). However, if only the tracks hitting the DNA target are taken into account, then the relative difference is more important for low energies and decreases to reach zero around 10 MeV. The computations were performed with models that contain up to 18,000 DNA nucleotide pairs. Nevertheless, DnaFabric will be extended to manipulate multi-scale models that go from the molecular to the cellular levels.

  1. Electrochemical impedance-based DNA sensor using a modified single walled carbon nanotube electrode

    International Nuclear Information System (INIS)

    Carbon nanotubes have become promising functional materials for the development of advanced electrochemical biosensors with novel features which could promote electron-transfer with various redox active biomolecules. This paper presents the detection of Salmonella enterica serovar Typhimurium using chemically modified single walled carbon nanotubes (SWNTs) with single stranded DNA (ssDNA) on a polished glassy carbon electrode. Hybridization with the corresponding complementary ssDNA has shown a shift in the impedance studies due to a higher charge transfer in ssDNA. The developed biosensor has revealed an excellent specificity for the appropriate targeted DNA strand. The methodologies to prepare and functionalize the electrode could be adopted in the development of DNA hybridization biosensor.

  2. Electrochemical impedance-based DNA sensor using a modified single walled carbon nanotube electrode

    Energy Technology Data Exchange (ETDEWEB)

    Weber, Jessica E. [Department of Mechanical Engineering, University of South Florida, Tampa, FL (United States); Nanomaterials and Nanomanufacturing Research Center, University of South Florida, Tampa, FL (United States); Pillai, Shreekumar [Center for NanoBiotechnology Research, Alabama State University, Montgomery, AL (United States); Ram, Manoj Kumar, E-mail: mkram@usf.edu [Department of Mechanical Engineering, University of South Florida, Tampa, FL (United States); Nanomaterials and Nanomanufacturing Research Center, University of South Florida, Tampa, FL (United States); Kumar, Ashok [Department of Mechanical Engineering, University of South Florida, Tampa, FL (United States); Nanomaterials and Nanomanufacturing Research Center, University of South Florida, Tampa, FL (United States); Singh, Shree R. [Center for NanoBiotechnology Research, Alabama State University, Montgomery, AL (United States)

    2011-07-20

    Carbon nanotubes have become promising functional materials for the development of advanced electrochemical biosensors with novel features which could promote electron-transfer with various redox active biomolecules. This paper presents the detection of Salmonella enterica serovar Typhimurium using chemically modified single walled carbon nanotubes (SWNTs) with single stranded DNA (ssDNA) on a polished glassy carbon electrode. Hybridization with the corresponding complementary ssDNA has shown a shift in the impedance studies due to a higher charge transfer in ssDNA. The developed biosensor has revealed an excellent specificity for the appropriate targeted DNA strand. The methodologies to prepare and functionalize the electrode could be adopted in the development of DNA hybridization biosensor.

  3. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

    DEFF Research Database (Denmark)

    Valentini, Alice; Taberlet, Pierre; Miaud, Claude;

    2016-01-01

    species detection from DNA present into the environment. In this study, we tested if an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony......Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for...... fish. The reliability of this method was cautiously validated in silico, in vitro, and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0...

  4. The unusual system of doubly uniparental inheritance of mtDNA: isn't one enough?

    Science.gov (United States)

    Breton, Sophie; Beaupré, Hélène Doucet; Stewart, Donald T; Hoeh, Walter R; Blier, Pierre U

    2007-09-01

    Mitochondria possess their own genetic material (mitochondrial DNA or mtDNA), whose gene products are involved in mitochondrial respiration and oxidative phosphorylation, transcription, and translation. In animals, mitochondrial DNA is typically transmitted to offspring by the mother alone. The discovery of 'doubly uniparental inheritance' (DUI) of mtDNA in some bivalves has challenged the paradigm of strict maternal inheritance (SMI). In this review, we survey recent advances in our understanding of DUI, which is a peculiar system of cytoplasmic DNA inheritance that involves distinct maternal and paternal routes of mtDNA transmission, a novel extension of a mitochondrial gene (cox2), recombination, and periodic 'role-reversals' of the normally male and female-transmitted mitochondrial genomes. DUI provides a unique opportunity for studying nuclear-cytoplasmic genome interactions and the evolutionary significance of different modes of mitochondrial inheritance. PMID:17681397

  5. Preparation of konjac glucomannan hydrogels as DNA-controlled release matrix.

    Science.gov (United States)

    Wen, Xian; Wang, Ting; Wang, Zhiyong; Li, Li; Zhao, Changsheng

    2008-04-01

    In this study, hydrogels for DNA-controlled release was prepared with konjac glucomannan (KGM), a water-soluble non-ionic polysaccharide, by means of deacetylated reaction and physically cross-linking method under mild conditions. The properties of the KGM hydrogels were analyzed by FTIR spectra and scanning electron microscopy (SEM). The integrality of the released DNA was investigated by circular dichroism (CD). The DNA release kinetics was performed using the DNA-loaded KGM gels in buffer solutions of pH 7.4 at 37+/-0.5 degrees C. Peppas model and Higuchi model were used to analysis the DNA release mechanism; the data indicated that the DNA release can be controlled by changing the preparation conditions and the structure parameters of the gels. This study suggested that the KGM hydrogels have a potential use for advanced controlled release. PMID:18190958

  6. Stimulation of mouse DNA primase-catalyzed oligoribonucleotide synthesis by mouse DNA helicase B.

    OpenAIRE

    Saitoh, A; S. Tada; Katada, T; Enomoto, T.

    1995-01-01

    Many prokaryotic and viral DNA helicases involved in DNA replication stimulate their cognate DNA primase activity. To assess the stimulation of DNA primase activity by mammalian DNA helicases, we analyzed the synthesis of oligoribonucleotides by mouse DNA polymerase alpha-primase complex on single-stranded circular M13 DNA in the presence of mouse DNA helicase B. DNA helicase B was purified by sequential chromatography through eight columns. When the purified DNA helicase B was applied to a M...

  7. Tops and Writhing DNA

    Science.gov (United States)

    Samuel, Joseph; Sinha, Supurna

    2011-04-01

    The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops to show that when subjected to stretch and twist, the polymer configurations which dominate the partition function admit a local writhe formulation in the spirit of Fuller and thus provide an underlying justification for the use of Fuller's "local writhe expression" which leads to considerable mathematical simplification in solving theoretical models of DNA and elucidating their predictions. Our result facilitates comparison of the theoretical models with single molecule micromanipulation experiments and computer simulations.

  8. Fleet DNA (Presentation)

    Energy Technology Data Exchange (ETDEWEB)

    Walkokwicz, K.; Duran, A.

    2014-06-01

    The Fleet DNA project objectives include capturing and quantifying drive cycle and technology variation for the multitude of medium- and heavy-duty vocations; providing a common data storage warehouse for medium- and heavy-duty vehicle fleet data across DOE activities and laboratories; and integrating existing DOE tools, models, and analyses to provide data-driven decision making capabilities. Fleet DNA advantages include: for Government - providing in-use data for standard drive cycle development, R&D, tech targets, and rule making; for OEMs - real-world usage datasets provide concrete examples of customer use profiles; for fleets - vocational datasets help illustrate how to maximize return on technology investments; for Funding Agencies - ways are revealed to optimize the impact of financial incentive offers; and for researchers -a data source is provided for modeling and simulation.

  9. Forensische DNA-Analytik

    OpenAIRE

    Jung, Sven

    2002-01-01

    Im Rahmen der vorliegenden Arbeit wurden verschiedene Möglichkeiten, die die mitochondriale DNA-Analytik für die Spurenkunde und die Populationsgenetik eröffnet, ausgelotet. Polymorphismen der beiden nichtcodierenden hypervariablen Regionen HV1 und HV2 wurden durch Sequenzierung erschlossen und ergaben zusammen für eine deutsche Populationsstichprobe (Unterfranken, n = 180) einen Diskriminationsindex (DI) von 0,99. Der DI betrug bei alleiniger Betrachtung der HV1 für eine deutsche (n = 198), ...

  10. Tops and Writhing DNA

    OpenAIRE

    Samuel, Joseph; Sinha, Supurna

    2010-01-01

    The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops...

  11. Radiobiology with DNA ligands

    International Nuclear Information System (INIS)

    The paper deals with the following topics: labelling of DNA ligands and other tumour-affinic compounds with 4.15-d 124I, radiotoxicity of Hoechst 33258 and 33342 and of iodinated Hoechst 33258 in cell cultures, preparation of 76Br-, 123I-, and 221At-labelled 5-halo-2'-deoxyuridine, chemical syntheses of boron derivatives of Hoechst 33258.III., Gadolinium neutron capture therapy

  12. A physicist's view of DNA

    CERN Document Server

    Mashaghi, Alireza

    2013-01-01

    Nucleic acids, like DNA and RNA, are molecules that are present in any life form. Their most notable function is to encode biological information. Why then would a physicist be interested in these molecules? As we will see, DNA is an interesting molecular tool for physicists to test and explore physical laws and theories, like the ergodic theorem, the theory of elasticity and information theory. DNA also has unique material properties, which attract material scientists, nanotechnologists and engineers. Among interesting developments in this field are DNA-based hybrid materials and DNA origami.

  13. DNA adducts-chemical addons

    OpenAIRE

    T. R. Rajalakshmi; N AravindhaBabu; Shanmugam, K. T.; Masthan, K. M. K.

    2015-01-01

    DNA adduct is a piece of DNA covalently bond to a chemical (safrole, benzopyrenediol epoxide, acetaldehyde). This process could be the start of a cancerous cell. When a chemical binds to DNA, it gets damaged resulting in abnormal replication. This could be the start of a mutation and without proper DNA repair, this can lead to cancer. It is this chemical that binds with the DNA is our prime area of concern. Instead of performing the whole body analysis for diagnosing cancer, this test could b...

  14. DNA nanotechnology and fluorescence applications.

    Science.gov (United States)

    Schlichthaerle, Thomas; Strauss, Maximilian T; Schueder, Florian; Woehrstein, Johannes B; Jungmann, Ralf

    2016-06-01

    Structural DNA nanotechnology allow researchers to use the unique molecular recognition properties of DNA strands to construct nanoscale objects with almost arbitrary complexity in two and three dimensions. Abstracted as molecular breadboards, DNA nanostructures enable nanometer-precise placement of guest molecules such as proteins, fluorophores, or nanoparticles. These assemblies can be used to study biological phenomena with unprecedented control over number, spacing, and molecular identity. Here, we give a general introduction to structural DNA nanotechnology and more specifically discuss applications of DNA nanostructures in the field of fluorescence and plasmonics. PMID:26773303

  15. DNA Nanobots as Cancer Treatment

    OpenAIRE

    Rahbek, Stephanie N. A; Laubacher, Alvine K. S; Løbner, Camilla J.; Gjermandsen, Niels-Henrik L.

    2016-01-01

    In the field of nanotechnology, there have been different ideas, on how the technology could enter the field of medicine. In this search, the DNA nanobot is the most promising. The DNA nanobot is complex in reality, but simple and elegant in thought. The concept consists of a drug delivery system, designed by DNA origami, where you fold DNA strands into a desirable shape in 3D, and thereafter place the drug inside. For the DNA nanobot to release the drug, the “locks” have to be activated, and...

  16. Involvement of DNA Damage Response Pathways in Hepatocellular Carcinoma

    Directory of Open Access Journals (Sweden)

    Sheau-Fang Yang

    2014-01-01

    Full Text Available Hepatocellular carcinoma (HCC has been known as one of the most lethal human malignancies, due to the difficulty of early detection, chemoresistance, and radioresistance, and is characterized by active angiogenesis and metastasis, which account for rapid recurrence and poor survival. Its development has been closely associated with multiple risk factors, including hepatitis B and C virus infection, alcohol consumption, obesity, and diet contamination. Genetic alterations and genomic instability, probably resulted from unrepaired DNA lesions, are increasingly recognized as a common feature of human HCC. Dysregulation of DNA damage repair and signaling to cell cycle checkpoints, known as the DNA damage response (DDR, is associated with a predisposition to cancer and affects responses to DNA-damaging anticancer therapy. It has been demonstrated that various HCC-associated risk factors are able to promote DNA damages, formation of DNA adducts, and chromosomal aberrations. Hence, alterations in the DDR pathways may accumulate these lesions to trigger hepatocarcinogenesis and also to facilitate advanced HCC progression. This review collects some of the most known information about the link between HCC-associated risk factors and DDR pathways in HCC. Hopefully, the review will remind the researchers and clinicians of further characterizing and validating the roles of these DDR pathways in HCC.

  17. Increasing global participation in genetics research through DNA barcoding.

    Science.gov (United States)

    Adamowicz, Sarah J; Steinke, Dirk

    2015-12-01

    DNA barcoding--the sequencing of short, standardized DNA regions for specimen identification and species discovery--has promised to facilitate rapid access to biodiversity knowledge by diverse users. Here, we advance our opinion that increased global participation in genetics research is beneficial, both to scientists and for science, and explore the premise that DNA barcoding can help to democratize participation in genetics research. We examine publication patterns (2003-2014) in the DNA barcoding literature and compare trends with those in the broader, related domain of genomics. While genomics is the older and much larger field, the number of nations contributing to the published literature is similar between disciplines. Meanwhile, DNA barcoding exhibits a higher pace of growth in the number of publications as well as greater evenness among nations in their proportional contribution to total authorships. This exploration revealed DNA barcoding to be a highly international discipline, with growing participation by researchers in especially biodiverse nations. We briefly consider several of the challenges that may hinder further participation in genetics research, including access to training and molecular facilities as well as policy relating to the movement of genetic resources. PMID:26642251

  18. Left-handed Z-DNA: structure and function

    Science.gov (United States)

    Herbert, A.; Rich, A.

    1999-01-01

    Z-DNA is a high energy conformer of B-DNA that forms in vivo during transcription as a result of torsional strain generated by a moving polymerase. An understanding of the biological role of Z-DNA has advanced with the discovery that the RNA editing enzyme double-stranded RNA adenosine deaminase type I (ADAR1) has motifs specific for the Z-DNA conformation. Editing by ADAR1 requires a double-stranded RNA substrate. In the cases known, the substrate is formed by folding an intron back onto the exon that is targeted for modification. The use of introns to direct processing of exons requires that editing occurs before splicing. Recognition of Z-DNA by ADAR1 may allow editing of nascent transcripts to be initiated immediately after transcription, ensuring that editing and splicing are performed in the correct sequence. Structural characterization of the Z-DNA binding domain indicates that it belongs to the winged helix-turn-helix class of proteins and is similar to the globular domain of histone-H5.

  19. Plant genome size variation: bloating and purging DNA.

    Science.gov (United States)

    Michael, Todd P

    2014-07-01

    Plant genome size variation is a dynamic process of bloating and purging DNA. While it was thought plants were on a path to obesity through continual DNA bloating, recent research supports that most plants activity purge DNA. Plant genome size research has greatly benefited from the cataloguing of genome size estimates at the Kew Plant DNA C-values Database, and the recent availability of over 50 fully sequenced and published plant genomes. The emerging trend is that plant genomes bloat due to the copy-and-paste proliferation of a few long terminal repeat retrotransposons (LTRs) and aggressively purge these proliferating LTRs through several mechanisms including illegitimate and incomplete recombination, and double-strand break repair through non-homologous end joining. However, ultra-small genomes such as Utricularia gibba (Bladderwort), which is 82 megabases (Mb), purge excess DNA through genome fractionation and neofunctionalization during multiple rounds of whole genome duplication (WGD). In contrast, the largest published genome, Picea abies (Norway Spruce) at 19 800 Mb, has no detectable WGD but has bloated with diverse and diverged LTRs that either have evaded purging mechanisms or these purging mechanism are absent in gymnosperms. Finally, advances in DNA methylation studies suggest that smaller genomes have a more aggressive epigenomic surveillance system to purge young LTR retrotransposons, which is less active or missing in larger genomes like the bloated gymnosperms. While genome size may not reflect genome complexity, evidence is mounting that genome size may reflect evolutionary status. PMID:24651721

  20. Cell-free circulating tumor DNA in cancer.

    Science.gov (United States)

    Qin, Zhen; Ljubimov, Vladimir A; Zhou, Cuiqi; Tong, Yunguang; Liang, Jimin

    2016-01-01

    Cancer is a common cause of death worldwide. Despite significant advances in cancer treatments, the morbidity and mortality are still enormous. Tumor heterogeneity, especially intratumoral heterogeneity, is a significant reason underlying difficulties in tumor treatment and failure of a number of current therapeutic modalities, even of molecularly targeted therapies. The development of a virtually noninvasive "liquid biopsy" from the blood has been attempted to characterize tumor heterogeneity. This review focuses on cell-free circulating tumor DNA (ctDNA) in the bloodstream as a versatile biomarker. ctDNA analysis is an evolving field with many new methods being developed and optimized to be able to successfully extract and analyze ctDNA, which has vast clinical applications. ctDNA has the potential to accurately genotype the tumor and identify personalized genetic and epigenetic alterations of the entire tumor. In addition, ctDNA has the potential to accurately monitor tumor burden and treatment response, while also being able to monitor minimal residual disease, reducing the need for harmful adjuvant chemotherapy and allowing more rapid detection of relapse. There are still many challenges that need to be overcome prior to this biomarker getting wide adoption in the clinical world, including optimization, standardization, and large multicenter trials. PMID:27056366

  1. Mitochondrial DNA in Sensitive Forensic Analysis

    OpenAIRE

    Nilsson, Martina

    2007-01-01

    Genetic profiling is commonly performed on the autosomes using multiple DNA markers. Although routine forensic DNA analysis is robust and based on reliable technologies, samples with degraded or limited amounts of DNA often fail. In these cases, the analysis of mitochondrial DNA (mtDNA) can be very valuable due to the high copy number per cell. This thesis describes evaluation and modifications of existing technologies that are useful in forensic DNA typing, mainly focusing on mtDNA. DNA quan...

  2. Advanced Aircraft Material

    Directory of Open Access Journals (Sweden)

    Vivek Kumar Prince

    2013-06-01

    Full Text Available There has been long debate on “advanced aircraft material” from past decades & researchers too came out with lots of new advanced material like composites and different aluminum alloys. Now days a new advancement that is in great talk is third generation Aluminum-lithium alloy. Newest Aluminum-lithium alloys are found out to have low density, higher elastic modulus, greater stiffness, greater cryogenic toughness, high resistance to fatigue cracking and improved corrosion resistance properties over the earlier used aircraft material as mentioned in Table 3 [1-5]. Comparison had been made with nowadays used composite material and is found out to be more superior then that

  3. Advanced materials-2007

    International Nuclear Information System (INIS)

    The 10th International Symposium on Advanced Materials (ISAM) was held from 3-7 September, 2007. From this symposium, material scientists and engineers can keep abreast with recent technologies involving advanced structural and functional materials. The proceeding of ISAM includes 94 papers which have been divided into six different sections: i) Development in material processing ii) Surface Engineering iii) phase transformation iv) advances in magnetic materials v) Nanotechnology and vi) reliability and life assessment. ISAM provides the opportunity to exchange technical know-how amongst Scientists, Engineers and researchers. (A.B.)

  4. Editorial: Advanced learning technologies

    Directory of Open Access Journals (Sweden)

    Yu-Ju Lan

    2012-03-01

    Full Text Available Recent rapid development of advanced information technology brings high expectations of its potential to improvement and innovations in learning. This special issue is devoted to using some of the emerging technologies issues related to the topic of education and knowledge sharing, involving several cutting edge research outcomes from recent advancement of learning technologies. Advanced learning technologies are the composition of various related technologies and concepts such as mobile technologies and social media towards learner centered learning. This editorial note provides an overview of relevant issues discussed in this special issue.

  5. Advanced healthcare materials

    CERN Document Server

    Tiwari, Ashutosh

    2014-01-01

    Advanced materials are attracting strong interest in the fundamental as well as applied sciences and are being extensively explored for their potential usage in a range of healthcare technological and biological applications. Advanced Healthcare Nanomaterials summarises the current status of knowledge in the fields of advanced materials for functional therapeutics, point-of-care diagnostics, translational materials, up and coming bio-engineering devices. The book highlights the key features which enable engineers to design stimuli-responsive smart nanoparticles, novel biomaterials, nan

  6. Compressive Sensing DNA Microarrays

    Directory of Open Access Journals (Sweden)

    Sheikh Mona A

    2009-01-01

    Full Text Available Compressive sensing microarrays (CSMs are DNA-based sensors that operate using group testing and compressive sensing (CS principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed.

  7. Forensic trace DNA: a review

    Directory of Open Access Journals (Sweden)

    van Oorschot Roland AH

    2010-12-01

    Full Text Available Abstract DNA analysis is frequently used to acquire information from biological material to aid enquiries associated with criminal offences, disaster victim identification and missing persons investigations. As the relevance and value of DNA profiling to forensic investigations has increased, so too has the desire to generate this information from smaller amounts of DNA. Trace DNA samples may be defined as any sample which falls below recommended thresholds at any stage of the analysis, from sample detection through to profile interpretation, and can not be defined by a precise picogram amount. Here we review aspects associated with the collection, DNA extraction, amplification, profiling and interpretation of trace DNA samples. Contamination and transfer issues are also briefly discussed within the context of trace DNA analysis. Whilst several methodological changes have facilitated profiling from trace samples in recent years it is also clear that many opportunities exist for further improvements.

  8. DNA adducts-chemical addons

    Directory of Open Access Journals (Sweden)

    T R Rajalakshmi

    2015-01-01

    Full Text Available DNA adduct is a piece of DNA covalently bond to a chemical (safrole, benzopyrenediol epoxide, acetaldehyde. This process could be the start of a cancerous cell. When a chemical binds to DNA, it gets damaged resulting in abnormal replication. This could be the start of a mutation and without proper DNA repair, this can lead to cancer. It is this chemical that binds with the DNA is our prime area of concern. Instead of performing the whole body analysis for diagnosing cancer, this test could be carried out for early detection of cancer. When scanning tunneling microscope is used, the DNA results can be obtained earlier. DNA adducts in scientific experiments are used as biomarkers.

  9. DNA adducts-chemical addons.

    Science.gov (United States)

    Rajalakshmi, T R; AravindhaBabu, N; Shanmugam, K T; Masthan, K M K

    2015-04-01

    DNA adduct is a piece of DNA covalently bond to a chemical (safrole, benzopyrenediol epoxide, acetaldehyde). This process could be the start of a cancerous cell. When a chemical binds to DNA, it gets damaged resulting in abnormal replication. This could be the start of a mutation and without proper DNA repair, this can lead to cancer. It is this chemical that binds with the DNA is our prime area of concern. Instead of performing the whole body analysis for diagnosing cancer, this test could be carried out for early detection of cancer. When scanning tunneling microscope is used, the DNA results can be obtained earlier. DNA adducts in scientific experiments are used as biomarkers. PMID:26015708

  10. DNA Methylation and Cancer Diagnosis

    Directory of Open Access Journals (Sweden)

    Jérôme Torrisani

    2013-07-01

    Full Text Available DNA methylation is a major epigenetic modification that is strongly involved in the physiological control of genome expression. DNA methylation patterns are largely modified in cancer cells and can therefore be used to distinguish cancer cells from normal tissues. This review describes the main technologies available for the detection and the discovery of aberrantly methylated DNA patterns. It also presents the different sources of biological samples suitable for DNA methylation studies. We discuss the interest and perspectives on the use of DNA methylation measurements for cancer diagnosis through examples of methylated genes commonly documented in the literature. The discussion leads to our consideration for why DNA methylation is not commonly used in clinical practice through an examination of the main requirements that constitute a reliable biomarker. Finally, we describe the main DNA methylation inhibitors currently used in clinical trials and those that exhibit promising results.

  11. Touch DNA-The prospect of DNA profiles from cables.

    Science.gov (United States)

    Lim, Sharon; Subhani, Zuhaib; Daniel, Barbara; Frascione, Nunzianda

    2016-05-01

    Metal theft in the railroad industry poses significant challenges to transport investigators. Cable sheaths left behind at crime scenes, if appropriately analysed, could provide valuable evidence in a forensic investigation, but attempts at recovering DNA are not routinely made. Experiments were set up to ascertain the success in DNA recovery from the surface of cable sheaths after deposition of (a) sweat, (b) extracted DNA and (c) fingermarks. Since investigators try to collect fingermarks and often treat the cables with cyanoacrylate fuming (CNA fuming) or wet powder suspensions (WPS) to enhance the marks this study investigated the recovery of DNA from fingermarks pre- and post-enhancement. The double-swab technique and mini-taping were compared as options to recover DNA from the cable sheaths. Results demonstrate that generally, there is no significant difference between using swabs or mini-tapes to recover the DNA from the non-porous cables (p>0.05). It was also illustrated that CNA fuming performed better than WPS in terms of subsequent recovery and profiling of DNA. CNA fuming resulted in an average increase in DNA recovered via swabbing and taping (more than 4× and 8×, respectively), as compared to no treatment, with 50% of the DNA recovered after CNA fuming generating full DNA profiles. PMID:27162019

  12. Investigating DNA Damage

    Science.gov (United States)

    Bush, Stephen P.; Hart, Peter E.; Russell, Eric M.

    2006-01-01

    Advances in the field of molecular biology, powered by a technological revolution, have increased dramatically over the past decades. Notable developments such as the cloning of adult sheep, the sequencing of the human genome, and the production of genetically modified organisms capture the attention of biologists, their students, and the general…

  13. Functionalizing Designer DNA Crystals

    Science.gov (United States)

    Chandrasekaran, Arun Richard

    Three-dimensional crystals have been self-assembled from a DNA tensegrity triangle via sticky end interaction. The tensegrity triangle is a rigid DNA motif containing three double helical edges connected pair-wise by three four-arm junctions. The symmetric triangle contains 3 unique strands combined in a 3:3:1 ratio: 3 crossover, 3 helical and 1 central. The length of the sticky end reported previously was two nucleotides (nt) (GA:TC) and the motif with 2-helical turns of DNA per edge diffracted to 4.9 A at beam line NSLS-X25 and to 4 A at beam line ID19 at APS. The purpose of these self-assembled DNA crystals is that they can be used as a framework for hosting external guests for use in crystallographic structure solving or the periodic positioning of molecules for nanoelectronics. This thesis describes strategies to improve the resolution and to incorporate guests into the 3D lattice. The first chapter describes the effect of varying sticky end lengths and the influence of 5'-phosphate addition on crystal formation and resolution. X-ray diffraction data from beam line NSLS-X25 revealed that the crystal resolution for 1-nt (G:C) sticky end was 3.4 A. Motifs with every possible combination of 1-nt and 2-nt sticky-ended phosphorylated strands were crystallized and X-ray data were collected. The position of the 5'-phosphate on either the crossover (strand 1), helical (strand 2), or central strand (3) had an impact on the resolution of the self-assembled crystals with the 1-nt 1P-2-3 system diffracting to 2.62 A at APS and 3.1 A at NSLS-X25. The second chapter describes the sequence-specific recognition of DNA motifs with triplex-forming oligonucleotides (TFOs). This study examined the feasibility of using TFOs to bind to specific locations within a 3-turn DNA tensegrity triangle motif. The TFO 5'-TTCTTTCTTCTCT was used to target the tensegrity motif containing an appropriately embedded oligopurine.oligopyrimidine binding site. As triplex formation involving cytidine

  14. Managing Advanced Parkinson Disease

    Science.gov (United States)

    ... well.” 11 Managing Advanced Parkinson Disease DENTAL CARE Oral hygiene should remain an important part of the daily routine in order to prevent serious dental problems and the development of other illnesses. The ...

  15. [Advanced resuscitation of adults

    DEFF Research Database (Denmark)

    Lippert, F.K.; Lauritsen, T.L.; Torp-Pedersen, C.

    2008-01-01

    International and European Resuscitation Council (ERC) Guidelines for Resuscitation 2005 implicate major changes in resuscitation, including new universal treatment algorithms. This brief summary of Guidelines 2005 for advanced resuscitation of adult cardiac arrest victims is based upon the ERC...

  16. Advance Care Planning

    Science.gov (United States)

    ... put on a breathing machine. Organ and tissue donation allows organs or body parts from a generally healthy person ... to your driver’s license. Some people also include organ donation in their advance care planning documents. At the ...

  17. Advanced functional materials

    CERN Document Server

    2011-01-01

    This book reviews the results of recent research on new materials arising from progress in polymer, ceramic, sensor, and fuel cell technology, including advanced inorganic-organic-hybrid polymeric materials, high functional sensor, and microbial fuel cells.

  18. Advanced Lab Consortium ``Conspiracy''

    Science.gov (United States)

    Reichert, Jonathan F.

    2006-03-01

    Advanced Laboratory instruction is a time-honored and essential element of an undergraduate physics education. But, from my vantage point, it has been neglected by the two major professional societies, APS and AAPT. At some schools, it has been replaced by ``research experiences,'' but I contend that very few of these experiences in the research lab, particularly in the junior year, deliver what they promise. It is time to focus the attention of APS, AAPT, and the NSF on the advanced lab. We need to create an Advanced Lab Consortium (ALC) of faculty and staff to share experiments, suppliers, materials, pedagogy, ideas, in short to build a professional network for those committed to advanced lab instruction. The AAPT is currently in serious discussions on this topic and my company stands ready with both financial and personnel resources to support the effort. This talk is a plea for co-conspirators.

  19. Advance Payment ACO Model

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Advance Payment Model is designed for physician-based and rural providers who have come together voluntarily to give coordinated high quality care to the...

  20. Advanced Missile Signature Center

    Data.gov (United States)

    Federal Laboratory Consortium — The Advanced Missile Signature Center (AMSC) is a national facility supporting the Missile Defense Agency (MDA) and other DoD programs and customers with analysis,...