Journal articles: 'Genomic DNA detection'

1

Bart, A. "Direct detection of methylation in genomic DNA." Nucleic Acids Research 33, no. 14 (August 2, 2005): e124-e124. http://dx.doi.org/10.1093/nar/gni121.

Full text

APA, Harvard, Vancouver, ISO, and other styles

2

Békési, Angéla, Eszter Holub, Hajnalka Laura Pálinkás, and Beáta G. Vértessy. "Detection of Genomic Uracil Patterns." International Journal of Molecular Sciences 22, no. 8 (April 9, 2021): 3902. http://dx.doi.org/10.3390/ijms22083902.

Full text

Abstract:

The appearance of uracil in the deoxyuridine moiety of DNA is among the most frequently occurring genomic modifications. Three different routes can result in genomic uracil, two of which do not require specific enzymes: spontaneous cytosine deamination due to the inherent chemical reactivity of living cells, and thymine-replacing incorporation upon nucleotide pool imbalances. There is also an enzymatic pathway of cytosine deamination with multiple DNA (cytosine) deaminases involved in this process. In order to describe potential roles of genomic uracil, it is of key importance to utilize efficient uracil-DNA detection methods. In this review, we provide a comprehensive and critical assessment of currently available uracil detection methods with special focus on genome-wide mapping solutions. Recent developments in PCR-based and in situ detection as well as the quantitation of genomic uracil are also discussed.

APA, Harvard, Vancouver, ISO, and other styles

3

Calcino, Andrew D., Nathan J. Kenny, and Marco Gerdol. "Single individual structural variant detection uncovers widespread hemizygosity in molluscs." Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1825 (April 5, 2021): 20200153. http://dx.doi.org/10.1098/rstb.2020.0153.

Full text

Abstract:

The advent of complete genomic sequencing has opened a window into genomic phenomena obscured by fragmented assemblies. A good example of these is the existence of hemizygous regions of autosomal chromosomes, which can result in marked differences in gene content between individuals within species. While these hemizygous regions, and presence/absence variation of genes that can result, are well known in plants, firm evidence has only recently emerged for their existence in metazoans. Here, we use recently published, complete genomes from wild-caught molluscs to investigate the prevalence of hemizygosity across a well-known and ecologically important clade. We show that hemizygous regions are widespread in mollusc genomes, not clustered in individual chromosomes, and often contain genes linked to transposition, DNA repair and stress response. With targeted investigations of HSP70-12 and C1qDC , we also show how individual gene families are distributed within pan-genomes. This work suggests that extensive pan-genomes are widespread across the conchiferan Mollusca, and represent useful tools for genomic evolution, allowing the maintenance of additional genetic diversity within the population. As genomic sequencing and re-sequencing becomes more routine, the prevalence of hemizygosity, and its impact on selection and adaptation, are key targets for research across the tree of life. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

APA, Harvard, Vancouver, ISO, and other styles

4

Zhang, Juan, Bernd Friebe, and Bikram S. Gill. "Detection of maize DNA sequences amplified in wheat." Genome 38, no. 5 (October 1, 1995): 946–50. http://dx.doi.org/10.1139/g95-124.

Full text

Abstract:

Genomic in situ hybridization to somatic metaphase chromosomes of hexaploid wheat cv. Chinese Spring using biotinylated maize genomic DNA as a probe revealed the existence of amplified maize DNA sequences in five pairs of chromosomes. The in situ hybridization sites were located on chromosomes 1A, 7A, 2B, 3B, and 7B. One pair of in situ hybridization sites was also observed in hexaploid oat. The locations and sizes of in situ hybridization sites varied among progenitor species.Key words: Triticum aestivum, Zea mays, shared DNA sequences, genomic in situ hybridization.

APA, Harvard, Vancouver, ISO, and other styles

5

Martins, S. A., M. D. Prazeres, L. P. Fonseca, and G. Monteiro. "DNA biosensors: towards a microparticle based-platform for genomic DNA detection." New Biotechnology 25 (September 2009): S19—S20. http://dx.doi.org/10.1016/j.nbt.2009.06.049.

Full text

APA, Harvard, Vancouver, ISO, and other styles

6

Mitra*, Tanushree, Shivshankar Kumdale, Sameer Chowdhary, and Amol D. Raut. "Sensitivity detection of Abacavir in human through SNP detection of HLA-B*5701 allele." International Journal of Bioassays 5, no. 08 (July 31, 2016): 4754. http://dx.doi.org/10.21746/ijbio.2016.08.006.

Full text

Abstract:

The main objective of this study was to make sure whether randomly taken 12 samples were sensitive to abacavir. The genomic DNA from 12 blood sample were extracted by phenol chloroform DNA extraction method, extracted genomic DNA were amplified and sequenced, thereafter SNPs were detected. Every sample had shown the presence of normal base at SNP position. This study indicated, those randomly taken 12 patients were sensitive to abacavir, so they can consume abacavir if they get infected with HIV.

APA, Harvard, Vancouver, ISO, and other styles

7

Browning, Heidi, Laura Berkowitz, Cynthia Madej, Janet E. Paulsen, Miriam E. Zolan, and Susan Strome. "Macrorestriction Analysis of Caenorhabditis elegans Genomic DNA." Genetics 144, no. 2 (October 1, 1996): 609–19. http://dx.doi.org/10.1093/genetics/144.2.609.

Full text

Abstract:

Abstract The usefulness of genomic physical maps is greatly enhanced by linkage of the physical map with the genetic map. We describe a “macrorestriction mapping” procedure for Caenarhabditis elegans that we have applied to this endeavor. High molecular weight, genomic DNA is digested with infrequently cutting restriction enzymes and size-fractionated by pulsed field gel electrophoresis. Southern blots of the gels are probed with clones from the C. elegans physical map. This procedure allows the construction of restriction maps covering several hundred kilobases and the detection of polymorphic restriction fragments using probes that map several hundred kilobases away. We describe several applications of this technique. (1) We determined that the amount of DNA in a previously uncloned region is <220 kb. (2) We mapped the mes-1 gene to a cosmid, by detecting polymorphic restriction fragments associated with a deletion allele of the gene. The 25-kb deletion was initially detected using as a probe sequences located ~400 kb away from the gene. (3) We mapped the molecular endpoint of the deficiency hDf6, and determined that three spontaneously derived duplications in the unc-38-dpy-5 region have very complex molecular structures, containing internal rearrangements and deletions.

APA, Harvard, Vancouver, ISO, and other styles

8

Minunni, Maria, Sara Tombelli, and Marco Mascini. "A Biosensor Approach for DNA Sequences Detection in Non‐amplified Genomic DNA." Analytical Letters 40, no. 7 (May 2007): 1360–70. http://dx.doi.org/10.1080/00032710701326718.

Full text

APA, Harvard, Vancouver, ISO, and other styles

9

Choi, Yong-Sung, Kyung-Sup Lee, and Dae-Hee Park. "Genomic detection using an indicator-free DNA on a DNA chip microarray." Current Applied Physics 6, no. 4 (July 2006): 772–76. http://dx.doi.org/10.1016/j.cap.2005.04.037.

Full text

APA, Harvard, Vancouver, ISO, and other styles

10

Greenbaum, J. A., S. C. J. Parker, and T. D. Tullius. "Detection of DNA structural motifs in functional genomic elements." Genome Research 17, no. 6 (June 1, 2007): 940–46. http://dx.doi.org/10.1101/gr.5602807.

Full text

APA, Harvard, Vancouver, ISO, and other styles

11

NISSAN, R., S. MAKKAR, M. SELA, and R. STEVENS. "Whole Genomic DNA Probe for Detection of Porphyromonas endodontalis." Journal of Endodontics 26, no. 4 (April 2000): 217–20. http://dx.doi.org/10.1097/00004770-200004000-00004.

Full text

APA, Harvard, Vancouver, ISO, and other styles

12

Myers, Richard M., Nadya Lumelsky, Leonard S. Lerman, and Tom Maniatis. "Detection of single base substitutions in total genomic DNA." Nature 313, no. 6002 (February 1985): 495–98. http://dx.doi.org/10.1038/313495a0.

Full text

APA, Harvard, Vancouver, ISO, and other styles

13

Zhang, Wenlong, Xiaodan Liu, Mengcheng Liu, Bo Ma, Li Xu, and Junwei Wang. "Development of a multiplex PCR for simultaneous detection of Pasteurella multocida, Mannheimia haemolytica and Trueperella pyogenes." Acta Veterinaria Hungarica 65, no. 3 (September 2017): 327–39. http://dx.doi.org/10.1556/004.2017.032.

Full text

Abstract:

Pasteurella multocida, Mannheimia haemolytica and Trueperella pyogenes are three bacterial pathogens closely associated with the bovine respiratory disease complex (BRDC). In the current study, a multiplex PCR for the simultaneous detection of these three bacteria in cultures was established. After serial optimisation, the detection limit of the method for the genomic DNA of the three bacteria was 40 pg/μl. The method could detect the genomic DNA of these three bacteria but not the genomic DNA of seven other bacterial strains. Together with the bacterial enrichment technology, the multiplex PCR could be used for detecting the three bacteria in animal tissues. This method might be valuable for speeding up laboratory diagnosis and directing the treatment of BRDC to these three bacterial pathogens.

APA, Harvard, Vancouver, ISO, and other styles

14

Mose, Lisle E., Charles M. Perou, and Joel S. Parker. "Improved indel detection in DNA and RNA via realignment with ABRA2." Bioinformatics 35, no. 17 (January 15, 2019): 2966–73. http://dx.doi.org/10.1093/bioinformatics/btz033.

Full text

Abstract:

Abstract Motivation Genomic variant detection from next-generation sequencing has become established as an extremely important component of research and clinical diagnoses in both cancer and Mendelian disorders. Insertions and deletions (indels) are a common source of variation and can frequently impact functionality, thus making their detection vitally important. While substantial effort has gone into detecting indels from DNA, there is still opportunity for improvement. Further, detection of indels from RNA-Seq data has largely been an afterthought and offers another critical area for variant detection. Results We present here ABRA2, a redesign of the original ABRA implementation that offers support for realignment of both RNA and DNA short reads. The process results in improved accuracy and scalability including support for human whole genomes. Results demonstrate substantial improvement in indel detection for a variety of data types, including those that were not previously supported by ABRA. Further, ABRA2 results in broad improvements to variant calling accuracy across a wide range of post-processing workflows including whole genomes, targeted exomes and transcriptome sequencing. Availability and implementation ABRA2 is implemented in a combination of Java and C/C++ and is freely available to all from: https://github.com/mozack/abra2. Supplementary information Supplementary data are available at Bioinformatics online.

APA, Harvard, Vancouver, ISO, and other styles

15

van den Broek, Evert, Stef van Lieshout, Christian Rausch, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Remond J. A. Fijneman, and Sanne Abeln. "GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes." F1000Research 5 (September 19, 2016): 2340. http://dx.doi.org/10.12688/f1000research.9259.1.

Full text

Abstract:

Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large) series of tumor samples. ‘GeneBreak’ is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH) or by (low-pass) whole genome sequencing (WGS). First, ‘GeneBreak’ collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, ‘GeneBreak’, is implemented in R (www.cran.r-project.org) and is available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/GeneBreak.html).

APA, Harvard, Vancouver, ISO, and other styles

16

van den Broek, Evert, Stef van Lieshout, Christian Rausch, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Remond J. A. Fijneman, and Sanne Abeln. "GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes." F1000Research 5 (July 6, 2017): 2340. http://dx.doi.org/10.12688/f1000research.9259.2.

Full text

Abstract:

Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large) series of tumor samples. ‘GeneBreak’ is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH) or by (low-pass) whole genome sequencing (WGS). First, ‘GeneBreak’ collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, ‘GeneBreak’, is implemented in R (www.cran.r-project.org) and is available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/GeneBreak.html).

APA, Harvard, Vancouver, ISO, and other styles

17

Kaewphinit, Thongchai, Somchai Santiwatanakul, Chamras Promptmas, and Kosum Chansiri. "Detection of Non-Amplified Mycobacterium tuberculosis Genomic DNA Using Piezoelectric DNA-Based Biosensors." Sensors 10, no. 3 (March 9, 2010): 1846–58. http://dx.doi.org/10.3390/s100301846.

Full text

APA, Harvard, Vancouver, ISO, and other styles

18

Porat, N., K. Bogdanov, A. Danielli, A. Arie, I. Samina, and A. Hadani. "Direct detection of chicken genomic DNA for gender determination by thymine-DNA glycosylase." British Poultry Science 52, no. 1 (February 2011): 58–65. http://dx.doi.org/10.1080/00071668.2010.549665.

Full text

APA, Harvard, Vancouver, ISO, and other styles

19

JANG, JUN HYEONG, SUN-JOONG KIM, BO HYUN YOON, JEE-HOON RYU, MAN BOCK GU, and HYO-IHL CHANG. "Detection of Alicyclobacillus Species in Fruit Juice Using a Random Genomic DNA Microarray Chip." Journal of Food Protection 74, no. 6 (June 1, 2011): 933–38. http://dx.doi.org/10.4315/0362-028x.jfp-10-418.

Full text

Abstract:

This study describes a method using a DNA microarray chip to rapidly and simultaneously detect Alicyclobacillus species in orange juice based on the hybridization of genomic DNA with random probes. Three food spoilage bacteria were used in this study: Alicyclobacillus acidocaldarius, Alicyclobacillus acidoterrestris, and Alicyclobacillus cycloheptanicus. The three Alicyclobacillus species were adjusted to 2 × 103 CFU/ml and inoculated into pasteurized 100% pure orange juice. Cy5-dCTP labeling was used for reference signals, and Cy3-dCTP was labeled for target genomic DNA. The molar ratio of 1:1 of Cy3-dCTP and Cy5-dCTP was used. DNA microarray chips were fabricated using randomly fragmented DNA of Alicyclobacillus spp. and were hybridized with genomic DNA extracted from Bacillus spp. Genomic DNA extracted from Alicyclobacillus spp. showed a significantly higher hybridization rate compared with DNA of Bacillus spp., thereby distinguishing Alicyclobacillus spp. from Bacillus spp. The results showed that the microarray DNA chip containing randomly fragmented genomic DNA was specific and clearly identified specific food spoilage bacteria. This microarray system is a good tool for rapid and specific detection of thermophilic spoilage bacteria, mainly Alicyclobacillus spp., and is useful and applicable to the fruit juice industry.

APA, Harvard, Vancouver, ISO, and other styles

20

Pascual, Lluís, Isabel Baroja, Elena Aznar, Félix Sancenón, M. Dolores Marcos, Jose Ramón Murguía, Pedro Amorós, Knut Rurack, and Ramón Martínez-Máñez. "Oligonucleotide-capped mesoporous silica nanoparticles as DNA-responsive dye delivery systems for genomic DNA detection." Chemical Communications 51, no. 8 (2015): 1414–16. http://dx.doi.org/10.1039/c4cc08306g.

Full text

APA, Harvard, Vancouver, ISO, and other styles

21

Vieira, Alexandre R., Kathleen B. Deeley, Nicholas F. Callahan, Jacqueline B. Noel, Ida Anjomshoaa, Wendy M. Carricato, Louise P. Schulhof, et al. "Detection of Streptococcus mutans Genomic DNA in Human DNA Samples Extracted from Saliva and Blood." ISRN Dentistry 2011 (April 10, 2011): 1–6. http://dx.doi.org/10.5402/2011/543561.

Full text

Abstract:

Caries is a multifactorial disease, and studies aiming to unravel the factors modulating its etiology must consider all known predisposing factors. One major factor is bacterial colonization, and Streptococcus mutans is the main microorganism associated with the initiation of the disease. In our studies, we have access to DNA samples extracted from human saliva and blood. In this report, we tested a real-time PCR assay developed to detect copies of genomic DNA from Streptococcus mutans in 1,424 DNA samples from humans. Our results suggest that we can determine the presence of genomic DNA copies of Streptococcus mutans in both DNA samples from caries-free and caries-affected individuals. However, we were not able to detect the presence of genomic DNA copies of Streptococcus mutans in any DNA samples extracted from peripheral blood, which suggests the assay may not be sensitive enough for this goal. Values of the threshold cycle of the real-time PCR reaction correlate with higher levels of caries experience in children, but this correlation could not be detected for adults.

APA, Harvard, Vancouver, ISO, and other styles

22

He, Peng, Xinhui Lou, Susan M. Woody, and Lin He. "Amplification-by-Polymerization in Biosensing for Human Genomic DNA Detection." ACS Sensors 4, no. 4 (April 3, 2019): 992–1000. http://dx.doi.org/10.1021/acssensors.9b00133.

Full text

APA, Harvard, Vancouver, ISO, and other styles

23

Shultzaberger, Ryan K., Rachel E. Abrams, Challise J. Sullivan, Anthony D. Schmitt, Thomas W. J. Thompson, and John Dresios. "Agnostic detection of genomic alterations by holistic DNA structural interrogation." PLOS ONE 13, no. 11 (November 29, 2018): e0208054. http://dx.doi.org/10.1371/journal.pone.0208054.

Full text

APA, Harvard, Vancouver, ISO, and other styles

24

D’Agata, Roberta, Giulia Breveglieri, Laura M. Zanoli, Monica Borgatti, Giuseppe Spoto, and Roberto Gambari. "Direct Detection of Point Mutations in Nonamplified Human Genomic DNA." Analytical Chemistry 83, no. 22 (November 15, 2011): 8711–17. http://dx.doi.org/10.1021/ac2021932.

Full text

APA, Harvard, Vancouver, ISO, and other styles

25

Armour, J. A. L., D. E. Barton, D. J. Cockburn, and G. R. Taylor. "The detection of large deletions or duplications in genomic DNA." Human Mutation 20, no. 5 (October 25, 2002): 325–37. http://dx.doi.org/10.1002/humu.10133.

Full text

APA, Harvard, Vancouver, ISO, and other styles

26

Xie, H. "Highly sensitive amperometric detection of genomic DNA in animal tissues." Nucleic Acids Research 32, no. 2 (January 21, 2004): 15e—15. http://dx.doi.org/10.1093/nar/gnh016.

Full text

APA, Harvard, Vancouver, ISO, and other styles

27

Kalidasan, Kamaladasan, Jia Ling Neo, and Mahesh Uttamchandani. "Direct visual detection of Salmonella genomic DNA using gold nanoparticles." Molecular BioSystems 9, no. 4 (2013): 618. http://dx.doi.org/10.1039/c3mb25527a.

Full text

APA, Harvard, Vancouver, ISO, and other styles

28

Taylor, M. A., K. S. Wise, and M. A. McIntosh. "Selective detection of Mycoplasma hyorhinis using cloned genomic DNA fragments." Infection and Immunity 47, no. 3 (1985): 827–30. http://dx.doi.org/10.1128/iai.47.3.827-830.1985.

Full text

APA, Harvard, Vancouver, ISO, and other styles

29

Novelli, Giuseppe, Ferdinando Mannello, and Bruno Dallapiccola. "PCR amplification and silver stain detection of genomic DNA fragments." Trends in Genetics 5 (1989): 293. http://dx.doi.org/10.1016/0168-9525(89)90109-1.

Full text

APA, Harvard, Vancouver, ISO, and other styles

30

Mulvaney, S. P., C. N. Ibe, C. R. Tamanaha, and L. J. Whitman. "Direct detection of genomic DNA with fluidic force discrimination assays." Analytical Biochemistry 392, no. 2 (September 2009): 139–44. http://dx.doi.org/10.1016/j.ab.2009.05.042.

Full text

APA, Harvard, Vancouver, ISO, and other styles

31

Borodina, Tatiana A., Hans Lehrach, and Aleksey V. Soldatov. "Ligation detection reaction-TaqMan procedure for single nucleotide polymorphism detection on genomic DNA." Analytical Biochemistry 333, no. 2 (October 2004): 309–19. http://dx.doi.org/10.1016/j.ab.2004.05.032.

Full text

APA, Harvard, Vancouver, ISO, and other styles

32

Mukai, Yasuhiko, Yumiko Nakahara, and Maki Yamamoto. "Simultaneous discrimination of the three genomes in hexaploid wheat by multicolor fluorescence in situ hybridization using total genomic and highly repeated DNA probes." Genome 36, no. 3 (June 1, 1993): 489–94. http://dx.doi.org/10.1139/g93-067.

Full text

Abstract:

Common wheat, Triticum aestivum, is an allohexaploid species consisting of three different genomes (A, B, and D). The three genomes were simultaneously discriminated with different colors. Biotinylated total genomic DNA of the diploid A genome progenitor Triticum urartu, digoxigenin-labeled total genomic DNA of the diploid D genome progenitor Aegilops squarrosa, and nonlabeled total genomic DNA of one of the possible B genome progenitors Ae. speltoides were hybridized in situ to metaphase chromosome spreads of Triticum aestivum cv. Chinese Spring. For detection, only two fluorochromes, fluorescein and rhodamine, were used. The A, B, and D genomes were simultaneously detected by their yellow, brown, and orange fluorescence, respectively. The genomic fluorescence in situ hybridization pattern of chromosome 4A of cv. Chinese Spring wheat showed that the distal 32% of the long arm was derived from a B genome chromosome. Furthermore, by using two highly repeated sequence probes, pSc 119.2 and pAsl, and two fluorochromes simultaneously, we were able to identify all B and D genome chromosomes and chromosomes 1A, 4A, and 5A of wheat.Key words: common wheat, in situ hybridization, multicolor fluorescence.

APA, Harvard, Vancouver, ISO, and other styles

33

Oueslati, Rania, Yu Jiang, Jiangang Chen, and Jayne Wu. "Rapid and Sensitive Point of Care Detection of MRSA Genomic DNA by Nanoelectrokinetic Sensors." Chemosensors 9, no. 5 (April 29, 2021): 97. http://dx.doi.org/10.3390/chemosensors9050097.

Full text

Abstract:

Biosensors have shown great potential in realizing rapid, low cost, and portable on-site detection for diseases. This work reports the development of a new bioelectronic sensor called AC electrokinetics-based capacitive (ABC) biosensor, for the detection of genomic DNA (gDNA) of methicillin-resistant Staphylococcus aureus (MRSA). The ABC sensor is based on interdigitated microelectrodes biofunctionalized with oligonucleotide probes. It uses a special AC signal for direct capacitive monitoring of topological change on nanostructured sensor surface, which simultaneously induces dielectrophoretic enrichment of target gDNAs. As a result, rapid and specific detection of gDNA/probe hybridization can be realized with high sensitivity. It requires no signal amplification such as labeling, hybridization chain reaction, or nucleic acid sequence-based amplification. This method involves only simple sample preparation. After optimization of nanostructured sensor surface and signal processing, the ABC sensor demonstrated fast turnaround of results (~10 s detection), excellent sensitivity (a detection limit of 4.7 DNA copies/µL MRSA gDNA), and high specificity, suitable for point of care diagnosis. As a bioelectronic sensor, the developed ABC sensors can be easily adapted for detections of other infectious agents.

APA, Harvard, Vancouver, ISO, and other styles

34

Rogaev, E. I., and A. B. Shlensky. "The genomic DNA øFd103 probe is sensitive marker for detection of human hypervariable genomic regions." Nucleic Acids Research 18, no. 4 (1990): 1081. http://dx.doi.org/10.1093/nar/18.4.1081.

Full text

APA, Harvard, Vancouver, ISO, and other styles

35

Sayyed, Danishmalik Rafiq, Satish Balasaheb Nimse, Keum-Soo Song, and Taisun Kim. "Detection of multiple mutations in a single codon of genomic DNA." Chem. Commun. 50, no. 82 (2014): 12344–47. http://dx.doi.org/10.1039/c4cc06220e.

Full text

APA, Harvard, Vancouver, ISO, and other styles

36

Maynard, Christine, Frédéric Berthiaume, Karine Lemarchand, Josée Harel, Pierre Payment, Paul Bayardelle, Luke Masson, and Roland Brousseau. "Waterborne Pathogen Detection by Use of Oligonucleotide-Based Microarrays." Applied and Environmental Microbiology 71, no. 12 (December 2005): 8548–57. http://dx.doi.org/10.1128/aem.71.12.8548-8557.2005.

Full text

Abstract:

ABSTRACT A small-oligonucleotide microarray prototype was designed with probes specific for the universal 16S rRNA and cpn60 genes of several pathogens that are usually encountered in wastewaters. In addition to these two targets, wecE-specific oligonucleotide probes were included in the microarray to enhance its discriminating power within the Enterobacteriaceae family. Universal PCR primers were used to amplify variable regions of 16S rRNA, cpn60, and wecE genes directly in Escherichia coli and Salmonella enterica serovar Typhimurium genomic DNA mixtures (binary); E. coli, S. enterica serovar Typhimurium, and Yersinia enterocolitica genomic DNA mixtures (ternary); or wastewater total DNA. Amplified products were fluorescently labeled and hybridized on the prototype chip. The detection sensitivity for S. enterica serovar Typhimurium was estimated to be on the order of 0.1% (104 S. enterica genomes) of the total DNA for the combination of PCR followed by microarray hybridization. The sensitivity of the prototype could be increased by hybridizing amplicons generated by PCR targeting genes specific for a bacterial subgroup, such as wecE genes, instead of universal taxonomic amplicons. However, there was evidence of PCR bias affecting the detection limits of a given pathogen as increasing amounts of a different pathogen were spiked into the test samples. These results demonstrate the feasibility of using DNA microarrays in the detection of waterborne pathogens within mixed populations but also raise the problem of PCR bias in such experiments.

APA, Harvard, Vancouver, ISO, and other styles

37

Knierim, Dennis, Quentin Barrière, Ioana Grigoras, Stephan Winter, Heinrich-Josef Vetten, Mark Schwinghamer, John Thomas, Paul Chu, Bruno Gronenborn, and Tatiana Timchenko. "Subterranean Clover Stunt Virus Revisited: Detection of Two Missing Genome Components." Viruses 11, no. 2 (February 4, 2019): 138. http://dx.doi.org/10.3390/v11020138.

Full text

Abstract:

Subterranean clover stunt virus (SCSV) is a type species of the genus Nanovirus in the family Nanoviridae. It was the first single-stranded DNA plant virus with a multipartite genome, of which genomic DNA sequences had been determined. All nanoviruses have eight genome components except SCSV, for which homologs of two genome components present in all other nanovirus genomes, DNA-U2 and DNA-U4, were lacking. We analysed archived and more recent samples from SCSV-infected legume plants to verify its genome composition and found the missing genome components. These results indicated that SCSV also has eight genome components and is a typical member of the genus Nanovirus.

APA, Harvard, Vancouver, ISO, and other styles

38

Li, Jin, Pasi A. Jänne, and G. Mike Makrigiorgos. "Biotinylated Probe Isolation of Targeted Gene Region Improves Detection of T790M Epidermal Growth Factor Receptor Mutation via Peptide Nucleic Acid–Enriched Real-Time PCR." Clinical Chemistry 57, no. 5 (May 1, 2011): 770–73. http://dx.doi.org/10.1373/clinchem.2010.157784.

Full text

Abstract:

BACKGROUND The presence of the EGFR (epidermal growth factor receptor) T790M mutation in tumor tissue or body fluids from patients treated with EGFR tyrosine kinase inhibitors may indicate the onset of resistance to treatment. It is important to identify this mutation as early as possible so that treatment can be modified accordingly or potential side effects of further treatment can be avoided. This requirement calls for high detection sensitivity. Peptide nucleic acids (PNAs) are used as PCR clamps to inhibit amplification of wild-type DNA during PCR cycling, thereby enriching for rare mutations such as T790M. We describe a modification that improves the detection limit of PNA-clamp methods by at least 20-fold. METHODS We enriched the target by exposing genomic DNA to an EGFR exon 20–specific biotinylated oligonucleotide, followed by binding to streptavidin beads. We then prepared serial dilutions of the isolated target DNA containing the T790M mutation by mixing with wild-type DNA and then performed PNA clamp–based, real-time TaqMan PCR. For comparison, we performed PNA clamp–based PCR directly on genomic DNA. RESULTS Whereas the detection limit for PNA clamp–based PCR performed directly on genomic DNA is 1 mutant allele in 1000 wild-type alleles, conducting the assay with biotinylated oligonucleotide–enriched target DNA improved the detection limit to 1 mutant allele in 40 000 wild-type alleles. A possible explanation for the improvement in detection is that biotin-based target isolation efficiently eliminates wild-type DNA; therefore, fewer erroneous amplifications of wild-type DNA can occur early during the PCR. CONCLUSIONS Combining target molecule isolation via a biotinylated probe with PNA-enriched TaqMan real-time PCR provides a major improvement for detecting the EGFR T790M resistance mutation.

APA, Harvard, Vancouver, ISO, and other styles

39

Jett, James H., Robert C. Habbersett, Xiaomei Yan, Thomas M. Yoshida, Babetta L. Marrone, and Richard A. Keller. "Sizing Dna Fragments by Ultrasensitive Flow Cytometry." Microscopy and Microanalysis 7, S2 (August 2001): 612–13. http://dx.doi.org/10.1017/s1431927600029135.

Full text

Abstract:

As originally developed in the 1960's, flow cytometry was primarily a technique for the analysis of mammalian cells. Analysis of cellular constituents such as DNA or cell surface antigens made fluorescent by a variety of reagents has been the main stay of flow cytometric applications. Over the years, flow cytometric analysis techniques have been developed that range from multicellular spheroids containing a million or more cells down to single molecule detection. An outgrowth of single molecule detection capability is DNA fragment size analysis.DNA fragment size analysis starts with a sample of naked DNA that can be derived from a variety of sources including PCR products, double stranded viral genomes, BAC/PAC clones, and bacterial genomes. For genomic or cloned DNA, restriction enzyme digests are analyzed to produce a fingerprint pattern. The fingerprint, i. e., the distribution of fragment sizes produced by the restriction enzyme digestion, is characteristic of the source of DNA and forms the basis for identifying the source.

APA, Harvard, Vancouver, ISO, and other styles

40

Mukai, Y., and B. S. Gill. "Detection of barley chromatin added to wheat by genomic in situ hybridization." Genome 34, no. 3 (June 1, 1991): 448–52. http://dx.doi.org/10.1139/g91-067.

Full text

Abstract:

A technique for in situ hybridization is reported that can be used to detect barley chromatin in wheat background using total genomic DNA as a probe. A 1:2 ratio of biotin-labeled genomic DNA of barley to blocking (unlabeled, sheared) DNA of wheat was sufficient to reveal brownish labeled barley chromosome domains against bluish background of unlabeled wheat chromatin in metaphase, prophase, and interphase nuclei of wheat-barley addition lines. Using this procedure, the behavior of specific barley chromosomes was analyzed in interphase and prophase cells. In prophase cells, the 6H chromosome was always associated with a nucleolus. A genomic clone of α-amylase gene (gRAmy56) that contains a barley-specific dispersed repeat sequence was also used to detect barley chromosomes in a wheat background.Key words: Hordeum vulgare, Triticum aestivum, genomic in situ hybridization, biotin, nucleolar organizing region.

APA, Harvard, Vancouver, ISO, and other styles

41

Abe, Aki, Kazuaki Inoue, Takeshi Tanaka, Junko Kato, Naoki Kajiyama, Ryuji Kawaguchi, Satoshi Tanaka, Makoto Yoshiba, and Michinori Kohara. "Quantitation of Hepatitis B Virus Genomic DNA by Real-Time Detection PCR." Journal of Clinical Microbiology 37, no. 9 (1999): 2899–903. http://dx.doi.org/10.1128/jcm.37.9.2899-2903.1999.

Full text

Abstract:

Quantitation of hepatitis B virus (HBV) DNA in serum is a useful method for the monitoring of HBV replication. We attempted to develop a quantitative assay system for HBV DNA that is more sensitive, accurate, and reproducible than existing systems. We detected HBV DNA by real-time detection PCR (RTD-PCR) based on Taq Man chemistry. The efficacy of this assay was evaluated by quantitatively measuring sequential levels of synthetic DNA and DNA in clinical serum samples. The detection limit of this system was as few as 10 DNA copies/reaction. A linear standard curve was obtained between 101 and 108 DNA copies/reaction. The coefficient of variation for both intra- and interexperimental variability indicated remarkable reproducibility. This system detected HBV DNA in 100% of chronic hepatitis B patients tested and never detected HBV DNA in healthy volunteers who were negative for HBV markers. These observations suggest that RTD-PCR is an excellent candidate for a standard HBV quantification method.

APA, Harvard, Vancouver, ISO, and other styles

42

Costanzo, G., R. Negri, E. Di Nicola-Negri, R. De Leo, and E. Di Mauro. "Detection of human genomic mutations by chemical single-reaction DNA sequencing." Technical Tips Online 2, no. 1 (January 1997): 32–34. http://dx.doi.org/10.1016/s1366-2120(08)70024-2.

Full text

APA, Harvard, Vancouver, ISO, and other styles

43

Singer, Alon, Meni Wanunu, Will Morrison, Heiko Kuhn, Maxim Frank-Kamenetskii, and Amit Meller. "Nanopore Based Sequence Specific Detection of Duplex DNA for Genomic Profiling." Nano Letters 10, no. 2 (February 10, 2010): 738–42. http://dx.doi.org/10.1021/nl100058y.

Full text

APA, Harvard, Vancouver, ISO, and other styles

44

Mosse, Yael P., Joel Greshock, Adam Margolin, Tara Naylor, Kristina Cole, Deepa Khazi, George Hii, et al. "High-resolution detection and mapping of genomic DNA alterations in neuroblastoma." Genes, Chromosomes and Cancer 43, no. 4 (August 2005): 390–403. http://dx.doi.org/10.1002/gcc.20198.

Full text

APA, Harvard, Vancouver, ISO, and other styles

45

Sumbal, Sumbal, Aneeqa Javed, Bakht Afroze, Hafiza Fizzah Zulfiqar, Faqeeha Javed, Sobia Noreen, and Bushra Ijaz. "Circulating tumor DNA in blood: Future genomic biomarkers for cancer detection." Experimental Hematology 65 (September 2018): 17–28. http://dx.doi.org/10.1016/j.exphem.2018.06.003.

Full text

APA, Harvard, Vancouver, ISO, and other styles

46

OMARUDDIN, Romaica A., and M. Ahmad CHAUDHRY. "Detection of genomic DNA methylation with denaturing high performance liquid chromatography." Human Cell 23, no. 2 (May 2010): 41–49. http://dx.doi.org/10.1111/j.1749-0774.2010.00084.x.

Full text

APA, Harvard, Vancouver, ISO, and other styles

47

Chen, TR, and C. Dorotinsky. "Non-radioactive detection of dot-blotted genomic DNA for species identification." Genetics Selection Evolution 23, Suppl 1 (1991): S85. http://dx.doi.org/10.1186/1297-9686-23-s1-s85.

Full text

APA, Harvard, Vancouver, ISO, and other styles

48

Lisitsyn, N. A., N. M. Lisitsina, G. Dalbagni, P. Barker, C. A. Sanchez, J. Gnarra, W. M. Linehan, B. J. Reid, and M. H. Wigler. "Comparative genomic analysis of tumors: detection of DNA losses and amplification." Proceedings of the National Academy of Sciences 92, no. 1 (January 3, 1995): 151–55. http://dx.doi.org/10.1073/pnas.92.1.151.

Full text

APA, Harvard, Vancouver, ISO, and other styles

49

Drážovská, Monika, Katarína Šiviková, Ján Dianovský, and Miroslav Horňák. "Comparative genomic hybridization in detection of DNA changes in canine lymphomas." Animal Science Journal 88, no. 1 (April 25, 2016): 27–32. http://dx.doi.org/10.1111/asj.12582.

Full text

APA, Harvard, Vancouver, ISO, and other styles

50

Padmavathy, Bakthavathsalam, Rajendran Vinoth Kumar, and Baquir Mohammed Jaffar Ali. "A direct detection of Escherichia coli genomic DNA using gold nanoprobes." Journal of Nanobiotechnology 10, no. 1 (2012): 8. http://dx.doi.org/10.1186/1477-3155-10-8.

Full text

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'Genomic DNA detection'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles