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Journal articles on the topic 'DNA sampling'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 February 2022

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1

Inoue, Eiji. "DNA Sampling and DNA Analysis of Chimpanzees at Mahale." Pan Africa News 12, no. 2 (2005): 22–24. http://dx.doi.org/10.5134/143454.

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2

Scriven, Jessica J., Lucy C. Woodall, and Dave Goulson. "Nondestructive DNA sampling from bumblebee faeces." Molecular Ecology Resources 13, no. 2 (2012): 225–29. http://dx.doi.org/10.1111/1755-0998.12036.

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3

Agorastos, T., K. Dinas, B. Lloveras, et al. "Self-sampling versus physician-sampling for human papillomavirus testing." International Journal of STD & AIDS 16, no. 11 (2005): 727–29. http://dx.doi.org/10.1258/095646205774763225.

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We evaluated the detection of human papillomavirus (HPV) infection using two sampling methods of cervical exfoliated cells, consisting of self-sampling of vaginal cells and cervical sampling performed by the physician. Women included were 379 patients of the general population attending outpatient clinics in Northern Greece for routine cytological cervical dysplasia screening. HPV DNA detection was similar with both sampling techniques. The HPV prevalences in self-collected samples were 4.7% and 3.7% in the physician-collected samples ( P>0.05). The Kappa statistic for HPV DNA agreement bet

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4

Lugg, William H., Josh Griffiths, Anthony R. Rooyen, Andrew R. Weeks, and Reid Tingley. "Optimal survey designs for environmental DNA sampling." Methods in Ecology and Evolution 9, no. 4 (2017): 1049–59. http://dx.doi.org/10.1111/2041-210x.12951.

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5

Thomsen, Philip Francis, Scott Elias, M. Thomas P. Gilbert, et al. "Non-Destructive Sampling of Ancient Insect DNA." PLoS ONE 4, no. 4 (2009): e5048. http://dx.doi.org/10.1371/journal.pone.0005048.

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6

Greenberg, Anthony J. "Fast Ordered Sampling of DNA Sequence Variants." G3: Genes|Genomes|Genetics 8, no. 5 (2018): 1455–60. http://dx.doi.org/10.1534/g3.117.300465.

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7

Zieger, Martin, Priscille Merciani Defaux, and Silvia Utz. "Electrostatic sampling of trace DNA from clothing." International Journal of Legal Medicine 130, no. 3 (2016): 661–67. http://dx.doi.org/10.1007/s00414-015-1312-1.

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8

Karolak, Aleksandra, and Arjan van der Vaart. "Enhanced sampling simulations of DNA step parameters." Journal of Computational Chemistry 35, no. 32 (2014): 2297–304. http://dx.doi.org/10.1002/jcc.23751.

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9

Stoop, Britta, Priscille Merciani Defaux, Silvia Utz, and Martin Zieger. "Touch DNA sampling with SceneSafe Fast™ minitapes." Legal Medicine 29 (November 2017): 68–71. http://dx.doi.org/10.1016/j.legalmed.2017.10.006.

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10

Smart, Adam S., Andrew R. Weeks, Anthony R. Rooyen, Alana Moore, Michael A. McCarthy, and Reid Tingley. "Assessing the cost‐efficiency of environmental DNA sampling." Methods in Ecology and Evolution 7, no. 11 (2016): 1291–98. http://dx.doi.org/10.1111/2041-210x.12598.

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11

Plante, Yves, Peter T. Boag, and Bradley N. White. "Nondestructive sampling of mitochondrial DNA from voles (Microtus)." Canadian Journal of Zoology 65, no. 1 (1987): 175–80. http://dx.doi.org/10.1139/z87-025.

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We present two techniques for sampling mitochondrial DNA (mtDNA) without killing individual voles. Total cellular DNA was extracted from small blood samples (100–250 μL) and tail segments (2 cm long) collected from meadow voles (Microtus pennsylvanicus). Restriction fragment patterns produced by the restriction endonucleases HindIII, BamH1, and EcoR1 after hybridization with a probe of nick-translated mtDNA compared well with standard mtDNA assays. Both techniques can be used in the field, and should prove useful in biochemical taxonomy as well as in investigations of population structure, dis

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12

Meyer, Christopher P., and Gustav Paulay. "DNA Barcoding: Error Rates Based on Comprehensive Sampling." PLoS Biology 3, no. 12 (2005): e422. http://dx.doi.org/10.1371/journal.pbio.0030422.

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13

DONALD, H. M., C. W. WOOD, K. M. BENOWITZ, R. A. JOHNSON, E. D. BRODIE, and V. A. FORMICA. "Nondestructive sampling of insect DNA from defensive secretion." Molecular Ecology Resources 12, no. 5 (2012): 856–60. http://dx.doi.org/10.1111/j.1755-0998.2012.03154.x.

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14

MURATA, KATSUMI, YUJI SUGITA, and YUKO OKAMOTO. "MOLECULAR DYNAMICS SIMULATIONS OF DNA DIMERS BASED ON REPLICA-EXCHANGE UMBRELLA SAMPLING I: TEST OF SAMPLING EFFICIENCY." Journal of Theoretical and Computational Chemistry 04, no. 02 (2005): 411–32. http://dx.doi.org/10.1142/s0219633605001611.

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In order to elucidate the stacking-unstacking process of DNA dimers, we have performed molecular dynamics simulations based on replica-exchange umbrella sampling (REUS), which is one of powerful conformational sampling techniques. We studied four DNA dimers composed of the adenine and thymine bases in both the 5′ and the 3′ positions (dApdA, dApdT, dTpdA, and dTpdT). We examined the time series of the distance between the glycosidic nitrogen atoms, root-mean-square deviations from A-DNA and B-DNA, various backbone and glycosidic torsion angles, and the pseudorotation phase angles as functions

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15

Smith, Brion C., Deborah L. Fisher, Victor W. Weedn, Gary R. Warnock, and Mitchell M. Holland. "A Systematic Approach to the Sampling of Dental DNA." Journal of Forensic Sciences 38, no. 5 (1993): 13524J. http://dx.doi.org/10.1520/jfs13524j.

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16

Curran, J. M., J. S. Buckleton, C. M. Triggs, and B. S. Weir. "Assessing uncertainty in DNA evidence caused by sampling effects." Science & Justice 42, no. 1 (2002): 29–37. http://dx.doi.org/10.1016/s1355-0306(02)71794-2.

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17

Thomas, Austen C., Jesse Howard, Phong L. Nguyen, Tracie A. Seimon, and Caren S. Goldberg. "eDNA Sampler: A fully integrated environmental DNA sampling system." Methods in Ecology and Evolution 9, no. 6 (2018): 1379–85. http://dx.doi.org/10.1111/2041-210x.12994.

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18

Ahrens, Dirk, Tomochika Fujisawa, Hans-Joachim Krammer, Jonas Eberle, Silvia Fabrizi, and Alfried P. Vogler. "Rarity and Incomplete Sampling in DNA-Based Species Delimitation." Systematic Biology 65, no. 3 (2016): 478–94. http://dx.doi.org/10.1093/sysbio/syw002.

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19

Chen, Tong, David E. A. Catcheside, Alice Stephenson, Chris Hefford, K. Paul Kirkbride, and Leigh A. Burgoyne. "A Rapid Wire-Based Sampling Method for DNA Profiling*." Journal of Forensic Sciences 57, no. 2 (2011): 472–77. http://dx.doi.org/10.1111/j.1556-4029.2011.02006.x.

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20

Ringler, Eva. "Testing skin swabbing for DNA sampling in dendrobatid frogs." Amphibia-Reptilia 39, no. 2 (2018): 245–51. http://dx.doi.org/10.1163/15685381-17000206.

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Abstract Skin swabbing, a minimally invasive DNA sampling method recently proposed for adult amphibians, was tested on the dendrobatid frog Allobates femoralis. I compared DNA yield from skin swabs and toe clips by evaluating obtained DNA concentrations and purity of extracts, as well as amplification success using eleven polymorphic microsatellite loci. I also tested whether storing skin swabs for two months at −20°C affected the properties of the extract or microsatellite analysis. Results show that skin swabs of adult A. femoralis suffered from high contamination and yielded significantly l

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21

Shepherd, Lara D. "A non-destructive DNA sampling technique for herbarium specimens." PLOS ONE 12, no. 8 (2017): e0183555. http://dx.doi.org/10.1371/journal.pone.0183555.

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22

Qi, Zhi, Sy Redding, Ja Yil Lee, et al. "DNA Sequence Alignment by Microhomology Sampling during Homologous Recombination." Cell 160, no. 5 (2015): 856–69. http://dx.doi.org/10.1016/j.cell.2015.01.029.

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23

Robinson, Anthony T., Yvette M. Paroz, Matthew J. Clement, et al. "Environmental DNA Sampling of Small‐Bodied Minnows: Performance Relative to Location, Species, and Traditional Sampling." North American Journal of Fisheries Management 39, no. 5 (2019): 1073–85. http://dx.doi.org/10.1002/nafm.10344.

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24

Karolak, Aleksandra, and Arjan van der Vaart. "Enhanced Sampling of DNA Step Parameters: Impact of Methylation on DNA Shape and Flexibility." Biophysical Journal 108, no. 2 (2015): 396a. http://dx.doi.org/10.1016/j.bpj.2014.11.2171.

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25

Mccartney, Carole. "Forensic DNA Sampling and the England and Wales National DNA Database: A Sceptical Approach." Critical Criminology 12, no. 2 (2004): 157–78. http://dx.doi.org/10.1023/b:crit.0000040255.29101.7a.

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26

Verdon, Timothy J., Kaye N. Ballantyne, R. John Mitchell, and Roland A. H. van Oorschot. "The Pinpoint DNA Isolation System as a novel DNA sampling method in forensic biology." Forensic Science International: Genetics Supplement Series 3, no. 1 (2011): e91-e92. http://dx.doi.org/10.1016/j.fsigss.2011.08.045.

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27

Siebers, Joerg, and A. Sarai. "Multicanonical Sampling of Protein-DNA Interactions Applied to Engrailed Homeodomain." Seibutsu Butsuri 41, supplement (2001): S184. http://dx.doi.org/10.2142/biophys.41.s184_2.

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28

Murata, K., Y. Sugita, and Y. Okamoto. "Free energy calculations of DNA base stacking using Replica-Exchange Umbrella Sampling." Seibutsu Butsuri 43, supplement (2003): S89. http://dx.doi.org/10.2142/biophys.43.s89_1.

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29

Feine, Ilan, Moshe Shpitzen, Boris Geller, et al. "Acetone facilitated DNA sampling from electrical tapes improves DNA recovery and enables latent fingerprints development." Forensic Science International 276 (July 2017): 107–10. http://dx.doi.org/10.1016/j.forsciint.2017.04.023.

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30

Mavigner, Maud, S. Thera Lee, Jakob Habib, et al. "Quantifying integrated SIV-DNA by repetitive-sampling Alu-gag PCR." Journal of Virus Eradication 2, no. 4 (2016): 219–26. http://dx.doi.org/10.1016/s2055-6640(20)30870-0.

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31

Churchill, G. A., J. J. Giovannoni, and S. D. Tanksley. "Pooled-sampling makes high-resolution mapping practical with DNA markers." Proceedings of the National Academy of Sciences 90, no. 1 (1993): 16–20. http://dx.doi.org/10.1073/pnas.90.1.16.

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32

Alberti, Federica, Javier Gonzalez, Johanna L. A. Paijmans, et al. "Optimized DNA sampling of ancient bones using Computed Tomography scans." Molecular Ecology Resources 18, no. 6 (2018): 1196–208. http://dx.doi.org/10.1111/1755-0998.12911.

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33

Baird, Patricia A. "Identifying People's Genes: Ethical Aspects of DNA Sampling in Populations." Perspectives in Biology and Medicine 38, no. 2 (1995): 159–66. http://dx.doi.org/10.1353/pbm.1995.0031.

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34

Carey, F. A., D. Lamb, and C. C. Bird. "Importance of sampling method in DNA analysis of lung cancer." Journal of Clinical Pathology 43, no. 10 (1990): 820–23. http://dx.doi.org/10.1136/jcp.43.10.820.

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35

Bergsten, J., D. T. Bilton, T. Fujisawa, et al. "The Effect of Geographical Scale of Sampling on DNA Barcoding." Systematic Biology 61, no. 5 (2012): 851–69. http://dx.doi.org/10.1093/sysbio/sys037.

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36

Chan, Hock Peng, Nancy Ruonan Zhang, and Louis H. Y. Chen. "Importance Sampling of Word Patterns in DNA and Protein Sequences." Journal of Computational Biology 17, no. 12 (2010): 1697–709. http://dx.doi.org/10.1089/cmb.2008.0233.

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37

Berg, Kåre. "DNA sampling and banking in clinical genetics and genetic research." New Genetics & Society 20, no. 1 (2001): 59–68. http://dx.doi.org/10.1080/14636770120010.1080/14636770120034646.

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38

Berg, Kåre. "DNA sampling and banking in clinical genetics and genetic research." New Genetics and Society 20, no. 1 (2001): 59–68. http://dx.doi.org/10.1080/14636770123300.

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39

Wilcox, T. M., K. J. Carim, M. K. Young, K. S. McKelvey, T. W. Franklin, and M. K. Schwartz. "Comment: The Importance of Sound Methodology in Environmental DNA Sampling." North American Journal of Fisheries Management 38, no. 3 (2018): 592–96. http://dx.doi.org/10.1002/nafm.10055.

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40

Goodnow, Robert A., Christoph E. Dumelin, and Anthony D. Keefe. "DNA-encoded chemistry: enabling the deeper sampling of chemical space." Nature Reviews Drug Discovery 16, no. 2 (2016): 131–47. http://dx.doi.org/10.1038/nrd.2016.213.

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41

Rong, Junkang, Jon S. Robertson, Stefan R. Schulze, and Andrew H. Paterson. "Cot-based sampling of genomes for polymorphic low-copy DNA." Molecular Breeding 32, no. 4 (2013): 977–80. http://dx.doi.org/10.1007/s11032-013-9964-3.

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42

Felczykowska, Agnieszka, Anna Krajewska, Sylwia Zielińska, and Joanna M. Łoś. "Sampling, metadata and DNA extraction - important steps in metagenomic studies." Acta Biochimica Polonica 62, no. 1 (2015): 151–60. http://dx.doi.org/10.18388/abp.2014_916.

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43

Mills, L. Scott, John J. Citta, Kevin P. Lair, Michael K. Schwartz, and David A. Tallmon. "ESTIMATING ANIMAL ABUNDANCE USING NONINVASIVE DNA SAMPLING: PROMISE AND PITFALLS." Ecological Applications 10, no. 1 (2000): 283–94. http://dx.doi.org/10.1890/1051-0761(2000)010[0283:eaaund]2.0.co;2.

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44

Chu, Jui-Hua, Hai-Yin Wu, Yi-Ju Yang, Osamu Takenaka, and Yao-Sung Lin. "Polymorphic microsatellite loci and low-invasive DNA sampling inMacaca cyclopis." Primates 40, no. 4 (1999): 573–80. http://dx.doi.org/10.1007/bf02574832.

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45

Hedman, Johannes, Joakim Ågren, and Ricky Ansell. "Crime scene DNA sampling by wet-vacuum applying M-Vac." Forensic Science International: Genetics Supplement Series 5 (December 2015): e89-e90. http://dx.doi.org/10.1016/j.fsigss.2015.09.036.

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46

Gibbon, Victoria E., Clem B. Penny, Goran Štrkalj, and Paul Ruff. "Brief communication: Minimally invasive bone sampling method for DNA analysis." American Journal of Physical Anthropology 139, no. 4 (2009): 596–99. http://dx.doi.org/10.1002/ajpa.21048.

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47

Sowalsky, Adam G. "SAMpling cancer development one carbon at a time." Science Translational Medicine 11, no. 484 (2019): eaax2731. http://dx.doi.org/10.1126/scitranslmed.aax2731.

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48

Immell, Dave, and Robert G. Anthony. "Estimation of Black Bear Abundance Using a Discrete DNA Sampling Device." Journal of Wildlife Management 72, no. 1 (2008): 324–30. http://dx.doi.org/10.2193/2006-297.

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49

Mes, Ted H. M., Nikolai Friesen, Reinhard M. Fritsch, Manfred Klaas, and Konrad Bachmann. "Criteria for Sampling in Allium Based on Chloroplast DNA PCR-RFLP'S." Systematic Botany 22, no. 4 (1997): 701. http://dx.doi.org/10.2307/2419436.

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50

McColl-Gausden, Emily F., Andrew R. Weeks, and Reid Tingley. "A field ecologist's guide to environmental DNA sampling in freshwater environments." Australian Zoologist 40, no. 4 (2020): 641–51. http://dx.doi.org/10.7882/az.2019.025.

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Environmental DNA, or eDNA—DNA shed from organisms and extracted from environmental samples—is an emerging survey technique that has the potential to transform biodiversity monitoring in freshwater ecosystems. We provide a brief overview of the primary methodological aspects of eDNA sampling that ecologists should consider before taking environmental samples in the field. We outline five key methodological considerations: (i) targeting single species vs multiple species; (ii) where and when to sample; (iii) how much water to collect; (iv) how many samples to take; and (v) recognising potential

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