Academic literature on the topic 'Random sequence DNA'
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Journal articles on the topic "Random sequence DNA"
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Sperling, Linda, Philippe Dessen, Marek Zagulski, Ron E. Pearlman, Andrzey Migdalski, Robert Gromadka, Marine Froissard, Anne-Marie Keller, and Jean Cohen. "Random Sequencing of Paramecium Somatic DNA." Eukaryotic Cell 1, no. 3 (June 2002): 341–52. http://dx.doi.org/10.1128/ec.1.3.341-352.2002.
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ABSTRACT We report a random survey of 1 to 2% of the somatic genome of the free-living ciliate Paramecium tetraurelia by single-run sequencing of the ends of plasmid inserts. As in all ciliates, the germ line genome of Paramecium (100 to 200 Mb) is reproducibly rearranged at each sexual cycle to produce a somatic genome of expressed or potentially expressed genes, stripped of repeated sequences, transposons, and AT-rich unique sequence elements limited to the germ line. We found the somatic genome to be compact (>68% coding, estimated from the sequence of several complete library inserts) and to feature uniformly small introns (18 to 35 nucleotides). This facilitated gene discovery: 722 open reading frames (ORFs) were identified by similarity with known proteins, and 119 novel ORFs were tentatively identified by internal comparison of the data set. We determined the phylogenetic position of Paramecium with respect to eukaryotes whose genomes have been sequenced by the distance matrix neighbor-joining method by using random combined protein data from the project. The unrooted tree obtained is very robust and in excellent agreement with accepted topology, providing strong support for the quality and consistency of the data set. Our study demonstrates that a random survey of the somatic genome of Paramecium is a good strategy for gene discovery in this organism.
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Banfalvi, Gaspar. "Origin of Coding RNA from Random-Sequence RNA." DNA and Cell Biology 38, no. 3 (March 2019): 223–28. http://dx.doi.org/10.1089/dna.2018.4389.
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Hsu, Tai-Hsin, and Su-Long Nyeo. "Simple Deviation Analysis of Two-Dimensional Viral DNA Walks." Journal of Biological Systems 11, no. 03 (September 2003): 221–43. http://dx.doi.org/10.1142/s0218339003000841.
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We consider the method of two-dimensional DNA walks based on three independent groups of mapping rules for 21 DNA sequences of animal and plant viruses, and for the sequences of irrational and random numbers. This method provides a visualization tool for the determination of the regional abundance of nucleotides in DNA sequences. By defining a statistical deviation and a maximum-deviation ratio for a DNA walk, we find that the maximum-deviation ratios for the 21 viral DNA sequences are generally larger than those of the random-number sequences of same lengths. It is shown that the viral DNA sequences generally have the smallest maximum-deviations with the same mapping group, and that greater difference between CG and AT contents is associated with larger maximum-deviation ratio. Also it is possible to distinguish a viral DNA sequence from a random-number sequence if the lengths of the sequences are longer than 2000 base-pairs. Other possible applications of the two-dimensional DNA walks are mentioned.
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Liu, Chang, Vladimir Vigdorovich, Vivek Kapur, and Mitchell S. Abrahamsen. "A Random Survey of the Cryptosporidium parvum Genome." Infection and Immunity 67, no. 8 (August 1, 1999): 3960–69. http://dx.doi.org/10.1128/iai.67.8.3960-3969.1999.
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ABSTRACT Cryptosporidium parvum is an obligate intracellular pathogen responsible for widespread infections in humans and animals. The inability to obtain purified samples of this organism’s various developmental stages has limited the understanding of the biochemical mechanisms important for C. parvum development or host-parasite interaction. To identify C. parvum genes independent of their developmental expression, a random sequence analysis of the 10.4-megabase genome of C. parvum was undertaken. Total genomic DNA was sheared by nebulization, and fragments between 800 and 1,500 bp were gel purified and cloned into a plasmid vector. A total of 442 clones were randomly selected and subjected to automated sequencing by using one or two primers flanking the cloning site. In this way, 654 genomic survey sequences (GSSs) were generated, corresponding to >320 kb of genomic sequence. These sequences were assembled into 408 contigs containing >250 kb of unique sequence, representing ∼2.5% of the C. parvum genome. Comparison of the GSSs with sequences in the public DNA and protein databases revealed that 107 contigs (26%) displayed similarity to previously identified proteins and rRNA and tRNA genes. These included putative genes involved in the glycolytic pathway, DNA, RNA, and protein metabolism, and signal transduction pathways. The repetitive sequence elements identified included a telomere-like sequence containing hexamer repeats, 57 microsatellite-like elements composed of dinucleotide or trinucleotide repeats, and a direct repeat sequence. This study demonstrates that large-scale genomic sequencing is an efficient approach to analyze the organizational characteristics and information content of the C. parvum genome.
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Lee, Suk-Hwan. "DNA sequence watermarking based on random circular angle." Digital Signal Processing 25 (February 2014): 173–89. http://dx.doi.org/10.1016/j.dsp.2013.11.010.
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Schriefer, Lawrence A., Beth K. Gebauer, Lisa Q. Q. Qiu, Robert H. Waterston, and Richard K. Wilson. "Low pressure DNA shearing: a method for random DNA sequence analysis." Nucleic Acids Research 18, no. 24 (1990): 7455–56. http://dx.doi.org/10.1093/nar/18.24.7455.
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Oliphant, A. R., C. J. Brandl, and K. Struhl. "Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein." Molecular and Cellular Biology 9, no. 7 (July 1989): 2944–49. http://dx.doi.org/10.1128/mcb.9.7.2944-2949.1989.
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We describe a new method for accurately defining the sequence recognition properties of DNA-binding proteins by selecting high-affinity binding sites from random-sequence DNA. The yeast transcriptional activator protein GCN4 was coupled to a Sepharose column, and binding sites were isolated by passing short, random-sequence oligonucleotides over the column and eluting them with increasing salt concentrations. Of 43 specifically bound oligonucleotides, 40 contained the symmetric sequence TGA(C/G)TCA, whereas the other 3 contained sequences matching six of these seven bases. The extreme preference for this 7-base-pair sequence suggests that each position directly contacts GCN4. The three nucleotide positions on each side of this core heptanucleotide also showed sequence preferences, indicating their effect on GCN4 binding. Interestingly, deviations in the core and a stronger sequence preference in the flanking region were found on one side of the central C . G base pair. Although GCN4 binds as a dimer, this asymmetry supports a model in which interactions on each side of the binding site are not equivalent. The random selection method should prove generally useful for defining the specificities of other DNA-binding proteins and for identifying putative target sequences from genomic DNA.
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Oliphant, A. R., C. J. Brandl, and K. Struhl. "Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein." Molecular and Cellular Biology 9, no. 7 (July 1989): 2944–49. http://dx.doi.org/10.1128/mcb.9.7.2944.
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We describe a new method for accurately defining the sequence recognition properties of DNA-binding proteins by selecting high-affinity binding sites from random-sequence DNA. The yeast transcriptional activator protein GCN4 was coupled to a Sepharose column, and binding sites were isolated by passing short, random-sequence oligonucleotides over the column and eluting them with increasing salt concentrations. Of 43 specifically bound oligonucleotides, 40 contained the symmetric sequence TGA(C/G)TCA, whereas the other 3 contained sequences matching six of these seven bases. The extreme preference for this 7-base-pair sequence suggests that each position directly contacts GCN4. The three nucleotide positions on each side of this core heptanucleotide also showed sequence preferences, indicating their effect on GCN4 binding. Interestingly, deviations in the core and a stronger sequence preference in the flanking region were found on one side of the central C . G base pair. Although GCN4 binds as a dimer, this asymmetry supports a model in which interactions on each side of the binding site are not equivalent. The random selection method should prove generally useful for defining the specificities of other DNA-binding proteins and for identifying putative target sequences from genomic DNA.
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MAVROTHALASSITIS, GEORGE, GREGORY BEAL, and TAKIS S. PAPAS. "Defining Target Sequences of DNA-Binding Proteins by Random Selection and PCR: Determination of the GCN4 Binding Sequence Repertoire." DNA and Cell Biology 9, no. 10 (December 1990): 783–88. http://dx.doi.org/10.1089/dna.1990.9.783.
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Bellini, T., G. Zanchetta, T. P. Fraccia, R. Cerbino, E. Tsai, G. P. Smith, M. J. Moran, D. M. Walba, and N. A. Clark. "Liquid crystal self-assembly of random-sequence DNA oligomers." Proceedings of the National Academy of Sciences 109, no. 4 (January 10, 2012): 1110–15. http://dx.doi.org/10.1073/pnas.1117463109.
Full textDissertations / Theses on the topic "Random sequence DNA"
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Roach, Jared C. "Random subcloning, pairwise end sequencing, and the molecular evolution of the vertebrate trypsinogens /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/8331.
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Smit, Rynhard. "Evaluation of Random Amplified Polymorphic DNA and Simple Sequence Repeat markers in Moringa oleifera (Lam.) to establish population diversity." Diss., University of Pretoria, 2013. http://hdl.handle.net/2263/43245.
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Moringa oleifera is potentially an economically important tree species. It has gained interest globally for its multipurpose uses, in particular as a source of nutrition and oil, as well as for its various medicinal properties. Moringa is native to India, Malaysia and the Middle East, but have been introduced to many countries throughout Africa. There is however limited knowledge regarding the genetic variation of both native and introduced populations of Moringa, although phenotypic observations suggest the presence of significant genetic diversity. To do this we used Moringa collections from different locations including India, South Africa and Hawaii, with different cultivars present in the foreign samples. Molecular markers such as Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeats (SSR) were evaluated for their efficiency as a marker system in Moringa, based on their success in other tropical tree population studies. The comparative analysis between the two revealed that both marker systems identified similar heterogeneity of 0.438 (RAPD) and 0.481 (SSR). However, the microsatellite marker was more effective for assessing genetic diversity, with a marker index (MI) value of 5.77 compared to 2.96 (RAPD), within our data set. Three major groups among the 71 accessions were clustered together in the dendogram and Principle Co-ordinate Analysis (PCoA), based on the genetic similarity matrices generated by both markers. Both cultivars were grouped together irrespective of origins, suggesting a relationship of genetic identity rather than geographical origins. The markers investigated in this study were found to be effective for determining genetic diversity, verifying higher genetic variation among the S.A. accessions of Moringas and distinguishing them from the cultivars investigated. This information could possibly be exploited for cultivar development in tree improvement programmes.Dissertation (MSc)--University of Pretoria, 2013.
lk2014
Genetics
MSc
Unrestricted
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Alamri, Sarah. "COMPARATIVE ANALYSIS OF SOYBEAN (GLYCINE MAX) ACCESSIONS USING INTER SIMPLE SEQUENCE REPEAT (ISSR) AND RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS." Thesis, Laurentian University of Sudbury, 2014. https://zone.biblio.laurentian.ca/dspace/handle/10219/2201.
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Soybean (Glycine max) is an important crop in the world in terms of total production and usage. It is also among the least diverse species. The main objectives of the present study were 1) to determine differences between ISSR and RAPD marker systems in detecting genetic variation in soybeans and 2) to identify and characterize accession- diagnostic molecular markers in G. max accessions. Genomic DNAs from 108 G. max accessions from 11 different gene pools were analyzed using several ISSR and RAPD primers. The levels of polymorphic loci detected with the two marker systems were in general moderate and similar.. Overall, 82% of genetic distance values were above 0.40 based on ISSR analysis. However, RAPD data revealed that the accessions from different countries are closely related with 64% genetic distance values below 0.40. The dendrograms constructed with ISSR data revealed that the South Korean accessions formed an out-group while the RAPD analysis showed that accessions from Sweden were separate from the other 10 gene pools. One variety-diagnostic marker generated with ISSR 5 primer was identified in the accession Kao Chien Tao from China. This marker was cloned, and sequenced. Although RAPD and ISSR marker systems detected similar levels of genetic variability, they target different regions of the soybean genome, resulting in different clustering of the 11 gene pools indicating different genetic relatedness among them. This finding demonstrates the usefulness of both marker systems in assessing diversity and relatedness among Glycine max gene pools.
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Rosen, Gail L. "Signal processing for biologically-inspired gradient source localization and DNA sequence analysis." Diss., Available online, Georgia Institute of Technology, 2006, 2006. http://etd.gatech.edu/theses/available/etd-07102006-123527/.
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Thesis (Ph. D.)--Electrical and Computer Engineering, Georgia Institute of Technology, 2007.Oliver Brand, Committee Member ; James H. McClellan, Committee Member ; Paul Hasler, Committee Chair ; Mark T. Smith, Committee Member ; David Anderson, Committee Member.
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DI, LEO SIMONE. "SELECTIVE ASSEMBLY, PHASE TRANSITIONS AND MOLECULAR KINETICS OF DNA OLIGOMERS." Doctoral thesis, Università degli Studi di Milano, 2022. http://hdl.handle.net/2434/923222.
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In the last few years it has been shown that the spontaneous self-assembly process of short DNA and RNA duplexes into liquid crystal ordering is a likely potential route that led to the formation of first nucleic acids able to support biological activities. In particular, it has been experimentally demonstrated that liquid crystal domains behave as suitable micro-reactors to trigger polymerization between the stacked and not initially chemically linked short nucleic acids. Even paired mononucleotides at high enough concentration exhibit liquid crystal ordering, unveiling the crucial role of Watson-Crick selectivity and stacking attractive interactions among base pairs. In such a possible prebiotic context, DNA sequences with both random nucleobases sequence and length are likely to be formed. Surprisingly, it has been shown that even random DNA sequence of fixed length can support liquid crystal ordering at high concentration.
The aim of this PhD thesis is to extend the knowledge of DNA liquid crystals self-assembly in the following four directions.
First, I explored the selectivity of interaction in nucleic acids solutions of random-sequence DNA oligomers of different length L. The combination of experimental results and a suitable developed theoretical model revealed a not negligible percentage of perfect duplexes.
Second, I investigated the process that leads to the onset of the nematic liquid crystal phase in aqueous solutions of DNA duplexes. The combination of static light scattering experiments and computer simulations made possible the study of both aggregation and local ordering of DNA duplexes in the isotropic phase, where no positional order is developed, and in proximity of the isotropic-nematic phase boundary. This study gives an insight of the role on the development of local orientational order among DNA duplexes both far and in proximity of the isotropic-nematic phase boundary.
Third, I studied the diffusion of short DNA duplexes with attractive and repulsive interactions in the isotropic phase as a function of temperature. I found that the temperature dependence of diffusion coefficients reflects via an Arrhenius law the interduplex attractive interactions, whereas diffusion of repulsive duplexes is partially well described in terms of repulsive hard spheres.
Fourth, I investigated phase diagrams of mixtures of DNA single strands and duplexes with various polycations that show liquid-liquid phase separations. This phenomena leads to the onset of a concentrated but still liquid phase of polyelectrolytes, called coacervate, in a bulk phase where polyelectrolytes are diluted. The most surprising result I found, it is the insurgence of liquid crystals in coacervates with 12 nucleobases long random DNA oligomers and polylysine at different ionic strengths.
I believe that this PhD thesis adds important pieces to the self-assembly of nucleic acids puzzle, and in particular it shows how randomness of nucleic acids is not an impasse to both hybridization of defectless duplexes and liquid crystal ordering.
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"Gene expression of adult human heart as revealed by random sequencing of cDNA library." Chinese University of Hong Kong, 1995. http://library.cuhk.edu.hk/record=b5895472.
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by Tsui Kwok-wing.Thesis (Ph.D.)--Chinese University of Hong Kong, 1995.
Includes bibliographical references (leaves 188-216).
ACKNOWLEDGEMENTS --- p.ii
ABSTRACT --- p.iii
TABLE OF CONTENTS --- p.v
ABBREVIATIONS --- p.ix
Chapter CHAPTER 1 --- INTRODUCTION
Chapter 1.1 --- General introduction --- p.1
Chapter 1.2 --- Human genome project --- p.5
Chapter 1.3 --- Organization of human genome --- p.7
Chapter 1.4 --- Adult human heart cDNA library --- p.9
Chapter 1.5 --- Gene expression in adult human heart --- p.10
Chapter 1.6 --- Polymerase chain reaction --- p.12
Chapter 1.7 --- Purification of PCR products --- p.15
Chapter 1.8 --- Automated DNA sequencing --- p.17
Chapter 1.9 --- Sequence analysis by electronic mail server --- p.21
Chapter 1.10 --- Effects of agar and agarose on Vent´ёØ and Taq DNA polymerases --- p.23
Chapter 1.11 --- Transcription factors and zinc finger proteins --- p.25
Chapter 1.12 --- LIM domain --- p.28
Chapter 1.13 --- Cysteine-rich intestinal protein --- p.30
Chapter CHAPTER 2 --- MATERIALS AND METHODS
Chapter 2.1 --- Plating out the adult human heart cDNA library --- p.32
Chapter 2.2 --- Amplification by polymerase chain reaction --- p.33
Chapter 2.3 --- Purification of the PCR products by Millipore filters --- p.35
Chapter 2.4 --- Elimination of the purification of the PCR products before sequencing --- p.36
Chapter 2.5 --- Cycle sequencing --- p.37
Chapter 2.6 --- Unicycle sequencing --- p.38
Chapter 2.7 --- Sequencing by T7 polymerase --- p.39
Chapter 2.8 --- Gel electrophoresis in the automated A.L.F. sequencer --- p.41
Chapter 2.9 --- Sequence analysis by commercially available softwares --- p.42
Chapter 2.10 --- Sequence analysis through electronic mail server --- p.44
Chapter 2.11 --- Database for storing the result of each clone --- p.46
Chapter 2.12 --- Effects of agar and agarose on Vent´ёØ and Taq DNA polymerase --- p.47
Chapter 2.13 --- Mini-preparation of plasmid DNA --- p.50
Chapter 2.14 --- Large scale preparation of plasmid DNA --- p.51
Chapter 2.15 --- Cloning the human cysteine rich heart protein (hCRHP) into the pAED4 vector --- p.53
Chapter 2.16 --- Expression of hCRHP in E coli --- p.56
Chapter 2.17 --- Northern hybridization --- p.58
Chapter 2.18 --- Partial protein sequencing of hCRHP --- p.59
Chapter CHAPTER 3 --- RESULTS
Chapter 3.1 --- The sequencing results of adult human heart cDNA clones --- p.60
Chapter 3.2 --- Accuracy of sequencing results --- p.63
Chapter 3.3 --- Catalogues of genes expressed in the adult human heart --- p.65
Chapter 3.4 --- Effects of agar and agarose on Vent´ёØ and Taq DNA polymerases --- p.94
Chapter 3.5 --- Elimination of the purification of the PCR products before sequencing --- p.102
Chapter 3.6 --- Sequence analysis of hCRHP --- p.104
Chapter 3.7 --- Northern hybridization of hCRHP --- p.109
Chapter 3.8 --- Expression of hCRHP in E. coli --- p.112
Chapter CHAPTER 4 --- DISCUSSION
Chapter 4.1 --- Random sequencing of adult human heart cDNA clones --- p.118
Chapter 4.2 --- Catalogues of genes expressed in the adult human heart --- p.130
Chapter 4.3 --- Gene expression in the adult human heart --- p.137
Chapter 4.4 --- Importance of nonhuman matches --- p.170
Chapter 4.5 --- Effects of agar and agarose on Vent´ёØ and Taq DNA polymerases --- p.177
Chapter 4.6 --- Elimination of the purification of the PCR products before sequencing --- p.180
Chapter 4.7 --- The possible role of CRIP and hCRHP --- p.184
Chapter 4.8 --- Future prospect --- p.186
REFERENCE --- p.188
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Horejsi, Thomas. "Random amplified polymorphic DNA and sequence characterized amplified regions for studies of genetic diversity and downy mildew resistance in cucumber." 1998. http://catalog.hathitrust.org/api/volumes/oclc/40327141.html.
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Thesis (Ph. D.)--University of Wisconsin--Madison, 1998.Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 130-140).
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Min, Tee See, and 鄭思敏. "Genetic Diversity in Colocasia and Xanthosoma Based on Morphological Traits, Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeats (SSR) Markers." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/28240061297483500453.
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碩士國立中興大學
園藝學系
93
Abstract The genetic diversity of 30 Colocasia (KCC) and 14 Xanthosoma (KCX) accessions collected from Taiwan and other places were evaluated by morphological traits, RAPD (randomly amplified polymorphic DNA) and SSR (simple sequence repeats). Data for 28 characters of shoot, 9 characters of corm and 2 indexes were subjected to a genetic diversity analysis and the UPGMA cluster analysis was performed. The 44 accessions were clustered into 2 groups according to genus with genetic similarity of 0.32. The Colocasia accessions were clustered into 3 subgroups. KCC175 was independence from other accessions with 0.57 similarities. The second subgroup was composed of 14 accessions with the genetic similarity of 0.52 which included accessions with whitish or green leaf vein, corm flesh with slightly fibrous and white in color. The others comprised the third subgroup with the genetic similarity beyond 0.66. Most of the accessions with purple leaf vein, corm flesh with very fibrous and purple in color were included in this group. A total of 221 RAPD bands, which a means of 10.4 band by each primer, were generated using 15 out of 88 primers in the RAPD analysis. The polymorphism was 98.2%. All accessions were clustered into 2 groups in the RAPD analysis. The similarity within KCX accessions was 0.85 compared to 0.71 within KCC accessions. All KCX accessions except KCX002 were indistinguishable. All KCC accessions were clustered into 8 subgroups. KCC131 and 132 were in the first subgroup with genetic similarity 0.71. KCC002, 004, 062 and 064 were the only accession in subgroup with 0.77, 0.81, 0.78 and 0.84 similarities respectively. The 4th subgroup consisted of KCC029 and 050 which similarity was 0.85. The 6th subgroup included KCC145, 169 and CHC01 with similarity 0.84. The largest subgroup included other 19 accessions with similarity 0.85. In analyzing KCC accessions from SSR results, a total of 73 bands were generated using 13 out of 49 primer pairs. The means of bands generated by a primer pairs was 5.2 and the polymorphism was 93.2%. Thirty accessions were clustered into 5 groups with similarity 0.72. The similarity of the first subgroup included KCC029, 050 and 062 was 0.74. KCC131 and 132 comprised the second group with similarity 0.96. The third group consisted of 6 accessions that had similarity 0.78 and the forth group consisted of KCC002, 004 and 064 with similarity 0.74. The similarity of the fifth group that composed of other 16 accessions had 0.72 similarity. Taro germplasm could be identified by morphology such as leaf blade margin color, leaf vein color, color of corm flesh, flesh fibre and number of cormels. The molecular markers could be used to analyze the accessions within groups. The genetic diversity of the 44 taro accessions could be identified by at least 2 RAPD primers or 4 SSR primer pairs.
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Tsai, Tzung-Yu, and 蔡宗育. "Genetic Diversity in butterhead and crisphead lettuce (Lactuca sativa L.) by using Morphological Traits, Random Amplified Polymorphic DNA (RAPD) and Sequence Characterized Amplified Regions (SCAR) Markers." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/59226251002783909910.
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碩士國立中興大學
園藝學系所
96
The genetic diversity of 31 butterhead (BUT) and 26 crisphead (CRP) accessions were evaluated by morphological traits, RAPD (Random Amplified Polymorphic DNA) and SCAR (Sequence Characterized Amplified Regions). Data for 19 morphological traits were subjected to a genetic diversity analysis, after which a UPGMA cluster analysis was performed. The 57 accessions were clustered into 2 groups according to type with genetic similarity of 0.38. The first group included 15 accessions form Tainan and 3 accessions form the National Germplasm of the USA, which were clustered into 5 subgroups with the similarity beyond 0.61. The second group included 10 crisphead and 26 butterhead accessions, which were clustered into 6 subgroups with the similarity beyond 0.70. A total of 271 RAPD bands, with a mean band of 9.3 for each primer, were generated using 29 out of 130 primers in the RAPD analysis. The polymorphism was 53.9%. All accessions were clustered into 3 groups in the RAPD analysis. The first group included 13 crisphead accessions form the Taiwan agricultural research institute(TARI) with the similarity 0.86. The second group including 15 accessions form the Tainan district agricultural research and extention station(TDARES)、3 accessions form USA and 3 butterhead accessions with the similarity 0.88. The first, second and fourth subgroups included crisphead accessions. The third and fifth subgroups included 3 butterhead accessions. The third group was composed of 23 butterhead accessions with a the similarity of 0.82. In analyzing results from SCAR of butterhead and crisphead accessions, a total of 100 bands were generated using 21 out of 51 primer pairs. The means of bands generated by a primer pairs was 4.8 and the polymorphism was 73%. The 57 accessions were clustered into 3 groups. The first group included 13 crisphead accessions form the TARI with the similarity 0.76. The second group including 15 accessions form TDARES with a similarity of 0.88. The third group was composed of 26 butterhead and 3 accessions the USA with a similarity of 0.88. The analysis of RAPD and SCAR result in the main group of the dendrogram showed a similarity of 0.78~0.86 based on RAPD markers and which the SCAR markers displayed a similarity 0.68~0.78. The analysis of RAPD and SCAR result in the subgroup of the dendrogram showed a similarity of 0.84~0.96 based on RAPD markers and which the SCAR markers displayed a similarity 0.88~0.97. Lettuce germplasm could be identified by morphological characteristics such as leaf color, leaf texture and head type. The molecular markers could be used to cluster accessions into groups by SCAR and subgroups by RAPD successfully.
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MARIESCHI, Matteo. "Identificazione di possibili sofisticazioni in preparati commerciali di origano Mediterraneo ed analisi genetica di Origanum spp. mediante marcatori molecolari genomici: Random Amplified Polymorphic DNA (RAPD) e Sequence Characterized Amplified Region (SCAR)." Doctoral thesis, 2010. http://hdl.handle.net/11381/2306929.
Full textBooks on the topic "Random sequence DNA"
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Slack, Jonathan. 6. Genes in evolution. Oxford University Press, 2014. http://dx.doi.org/10.1093/actrade/9780199676507.003.0006.
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‘Genes in evolution’ illustrates that a great deal of change in the primary sequence of DNA was not adaptive at all. It was not natural selection, but ‘neutral evolution’, consisting of an accumulation of mutations of no selective consequence that spread through the population by the effects of random sampling of variants from one generation to the next. In natural selection, generally what is good for the organism is good for the propagation of the gene variants it carries. But sometimes, as for sex and altruism, maximizing inheritance of gene variants that bring them about seems at first sight to be of advantage to the group, but of disadvantage for the individual.
Book chapters on the topic "Random sequence DNA"
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Afify, Farag M., and Kamel Hussein Rahouma. "Applying Machine Learning for Securing Data Storage Using Random DNA Sequences and Pseudo-Random Sequence Generators." In Advances in Intelligent Systems and Computing, 286–98. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-69717-4_29.
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Joshi, Kalpana, and Preeti Chavan. "Development of Sequence Characterized Amplified Region from Random Amplified Polymorphic DNA Amplicons." In Methods in Molecular Biology, 123–34. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-609-8_10.
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Mahatma, Mahesh K., Vishal S. Srivashtav, and Sanjay Jha. "Genetic Diversity Analysis of Date Palm Using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR)." In Methods in Molecular Biology, 105–12. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7159-6_10.
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El Sharabasy, Sherif F., and Khaled A. Soliman. "Molecular Analysis of Date Palm Genetic Diversity Using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeats (ISSRs)." In Methods in Molecular Biology, 143–52. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7159-6_13.
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Haider, Nadia. "Determining Phylogenetic Relationships Among Date Palm Cultivars Using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) Markers." In Methods in Molecular Biology, 153–72. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7159-6_14.
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Tran, Dang Hung, Tho Hoan Pham, Kenji Satou, and Tu Bao Ho. "Conditional Random Fields for Predicting and Analyzing Histone Occupancy, Acetylation and Methylation Areas in DNA Sequences." In Lecture Notes in Computer Science, 221–30. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11732242_20.
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Beyene Goonde, Diriba, and Seltene Abady. "Marker Assisted Selection in Groundnut." In DNA Replication - Mechanisms, Epigenetics, and Gene Therapy Applications [Working Title]. IntechOpen, 2023. http://dx.doi.org/10.5772/intechopen.108476.
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Groundnut (Arachis hypogaea L.) is an important oilseed crop worldwide. Objective of this review is to highlight molecular breeding approach such as marker assisted selection on groundnut improvement with future perspectives. The review analyzed application of marker assisted selection including simple sequence repeats, random amplified polymorphism DNAs, single nucleotide polymorphism, amplified fragment length polymorphism and inter simple sequence repeats on groundnut improvement. Among the molecular markers, random amplified polymorphic DNA is a rapid method for developing genetic maps and to determine DNA fragments to characterize peanut cultivars. DArTseq is used for SNP discovery and genotyping, which enables considerable discovery of SNPs in a wide variety of non-model organisms and provides measures of genetic divergence. Polymorphism screening performed using these newly developed SSRs will greatly increase the density of SSR markers in the peanut genetic map in the future.
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Milosavljević, Aleksandar. "Discovering Patterns in DNA Sequences by the Algorithmic Significance Method." In Pattern Discovery in Biomolecular Data. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780195119404.003.0006.
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The parsimony method for reconstruction of evolutionary trees (Sober, 1988) and the minimal edit distance method for DNA sequence alignments (e.g., Waterman, 1984) are both based on the principle of Occam’s Razor (e.g., Losee, 1980; also known as the Parsimony principle). This principle favors the most concise theories among the multitudes that can possibly explain observed data. The conciseness may be measured by the number of postulated mutations within an evolutionary tree, by the number of edit operations that transform one DNA sequence into the other, or by another implicit or explicit criterion. A very general mathematical formulation of Occam’s Razor has been proposed via minimal length encoding by computer programs (for recent reviews, see Cover and Thomas, 1991; Li and Vitányi, 1993). Algorithmic significance is a general method for pattern discovery based on Occam’s Razor. The method measures parsimony in terms of encoding length, in bits, of the observed data. Patterns are defined as datasets that can be concisely encoded. The method is not limited to any particular class of patterns; the class of patterns is determined by specifying an encoding scheme. To illustrate the method, consider the following unusual discovery experiment: . . . 1. Pick a simple pseudorandom generator for digits from the set {0, 1, 2, 3}. 2. Pick a seed value for the generator and run it to obtain a sequence of 1000 digits; convert the digits to a DNA sequence by replacing all occurrences of digit 0 by letter A, 1 by G, 2 by C, and 3 by T. 3. Submit the sequence to a similarity search against a database containing a completely sequenced genome of a particular organism. . . . Assume that after an unspecified number of iterations of the three steps, with each iteration involving a different random generator or seed value or both, the search in the third step finally results in a genomic sequence highly similar to the query sequence. Does the genomic sequence contain a pattern? To argue for the presence of a pattern, one may directly apply the algorithmic significance method.
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KWAK, J. M., and H. G. NAM. "Generation of Expressed Sequence Tags of Brassica napus by Single-run Partial Sequencing of Random cDNA Clones." In Automated DNA Sequencing and Analysis, 120–22. Elsevier, 1994. http://dx.doi.org/10.1016/b978-0-08-092639-1.50022-8.
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Erlich, Henry. "In the Beginning." In Silent Witness, 15–33. Oxford University Press, 2020. http://dx.doi.org/10.1093/oso/9780190909444.003.0002.
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Chapter 1 reviews the history of DNA analysis for individual identification in criminal cases. The principles underlying Restriction Fragment Length Polymorphism (RFLP) and Polymerase Chain Reaction (PCR) and their application in the first cases in the US and the UK in the mid-‘80s are discussed. The differences between these two DNA technologies (RFLP and PCR) are discussed and the evolution of new PCR-based genotyping methods for analyzing length and sequence polymorphisms is reviewed. The first DNA exoneration, which used the PCR-based HLA-DQ alpha test, is discussed in the context of exclusionary and inclusionary DNA results. The statistical issues involved in interpreting a match (inclusion) between the genetic profile of the evidence and the reference samples by calculating the Random Match Probability metric is discussed. Finally, the contentious history of the debate about the admissibility of DNA results in the courtroom, known as the “DNA Wars” is reviewed.
Conference papers on the topic "Random sequence DNA"
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Kaipa, Kalyan Kumar, Kyusang Lee, Taejin Ahn, and Rangavittal Narayanan. "System for random access DNA sequence compression." In 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). IEEE, 2010. http://dx.doi.org/10.1109/bibmw.2010.5703942.
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Khalifa, Amal. "A Blind DNA-Steganography Approach using Ciphering and Random Sequence Splicing." In 2020 10th International Conference on Information Science and Technology (ICIST). IEEE, 2020. http://dx.doi.org/10.1109/icist49303.2020.9202036.
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Ismael, Yaseen. "Secure Image Steganography by Utilizing DNA Properties." In 3rd International Conference of Mathematics and its Applications. Salahaddin University-Erbil, 2020. http://dx.doi.org/10.31972/ticma22.08.
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In the last period, Steganography is commonly used as an alternative to encryption to achieve secret communication between parties. Many methods have emerged to achieve steganography, including the use of spatial domain, spread spectrum, transform domain, and etc. On the other hand, the methods of attackers have also developed in revealing hidden data and trying to retrieve it. To increase the security of the hiding process, some researchers have found hybrid methods that combine encryption and steganography processes. The research aims to present a new method in steganography by taking advantage of the properties of DNA, which includes the random sequence of nitrogenous bases (A, C, G, T), the process of hybridization, which occurs between two single strands of DNA to form a double strand of DNA so that the bases in the first strand are complementary to the nitrogenous bases in the second strand. The research includes the following steps: First, the secret image to be hidden is encrypted by encoding it into a series of nitrogenous bases, and then the XOR process is performed with a nitrogenous bases sequence for a DNA tape agreed upon between the sender and recipient, the hybridization process applied before and after the XOR process. The results show that encrypted image is much different from the original image and thus they added another level of security to the hidden image. Secondly, the encrypted image resulting from the first step is hidden in the cover image and using a new method based on the use of the agreed-upon DNA tape as a key.
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Labat, Ivan, and Radoje Drmanac. "SIMULATIONS OF ORDERING AND SEQUENCE RECONSTRUCTION OF RANDOM DNA CLONES HYBRIDIZED WITH A SMALL NUMBER OF OLIGOMERIC PROBES." In Proceedings of the 2nd International Conference. WORLD SCIENTIFIC, 1993. http://dx.doi.org/10.1142/9789814503655_0046.
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Frazier, D., Shu Wha Lin, J. Ware, Kenneth Smith, Howard Reisner, M. DeSerres, A. Wallmark, R. Ljung, I. M. Nilsson, and D. W. Stafford. "MAPPING OF 6 MONOCLONAL ANTIBODIES TO HUMAN FACTOR IX." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643565.
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In order to map the regions of human factor IX recognized by monoclonal antibodies we have inserted random fragments of the coding region of the cDNA for human factor IX into the lambda phage expression vector, lambda gtll. The resultant recombinant phage were screened with monoclonal antibodies, the immunoreactive phage were isolated, and the DNA of the inserted fragment was sequenced to determine which amino acids were immunoreactive. This data, coupled with data obtained from the use of specific fragments of human factor IX expressed in E. coli from a T7 phage promoter, has allowed us to map the location of several epitopes on the surface of the factor IX molecule. In those cases where the antibodies are specific for human factor IX, additional narrowing of the epitope is possible by comparing the amino acid sequence of human factor IX to the bovine molecule. Six monoclonal antibodies from 3 different laboratories have been mapped. The immunodominant epitopes appear to be the amino terminus of the activation peptide, the amino terminus of the heavy chain and the epidermal growth factor domains.
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O'hara, Patrick J., Frank A. Grant, A. Betty, J. Haldmen, and Mark J. Murray. "Structure of the Human Factor VII Gene." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643786.
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Factor VII is a member of a family of vitamin K-dependent, gamma-carboxylated plasma protein which includes factor IX, factor X, protein C, protein S and prothrombin. Activated factor VII (factor Vila) is a plasma serine protease which participates in a cascade of reactions leading to the coagulation of blood. Two overlapping genomic clones containing sequences encoding human factor VII were isolated and characterized. The complete sequence of the gene was determined and found to span 12.8 kilobases. The mRNA for factor VII as demonstrated by cDNA cloning is polyadenylated at multiple sites but contains only one AAUAAA poly-A signal sequence. The mRNA can undergo alternative splicing forming one transcript containing eight segments as exons and another with an additional exon which encodes a larger pre-pro leader sequence. The portion of the pre-pro leader coded for by the additional exon has no known counterpart in the other vitamin K-dependent proteins. The positions of the introns with respect to the amino acid sequence encoded by the eight essential exons of factor VII are the same as those present in factor IX, factor X, protein C and the first three exons of prothrombin. These exons code for domains generally conserved among members of this gene family, including a pre-pro leader (the essential exon la and alternative exon lb), a gamma-carboxylated domain (exons 2 and 3) a growth factor domain (exons 4 and 5) an activation region (exon 6) and a serine protease (exon 8). The corresponding introns in these genes are dissimilar with respect to size and sequence, with the exception of the third intron in factor VII and protein C. Four introns and a portion of exon 8 in factor VII contain regions made up of tandem repeats of oligonucleotide monomer elements. More than a quarter of the intron sequences and more than a third of the 3' untranslated portion of the mRNA transcript consist of these minisatellite tandem repeats. This type of structure is responsible for polymorphisms due to allelic variation in repeat copy number in other areas of the human genome. Tandem repeats can evolve as a result of random crossover in DNA whose sequence is not maintained by selection. This suggests that much of the sequence information present in the introns and untranslated portion of the message is dispensable.
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Pannekoek, H., M. Linders, J. Keijer, H. Veerman, H. Van Heerikhuizen, and D. J. Loskutoff. "THE STRUCTURE OF THE HUMAN ENDOTHELIAL PLASMINOGEN ACTIVATOR INHIBITOR (PAI-1) GENE: NON-RANDOM POSITIONING OF INTRONS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644767.
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The endothelium plays a crucial role in the regulation of the fibrinolytic process, since it synthesizes and secretes tissue-type plasminogen activator (t-PA) as well as the fast-acting plasminogen activator inhibitor (PAI-1). Molecular cloning of full-length PAI-1 cDNA, employing a human endothelial cDNA expression library, and a subsequent determination of the complete nucleotide sequence, allowed a prediction of the amino-acid sequence of the PAI-1 glycoprotein. It was observed that the amino-acid sequence is significantly homologous to those of members of the serine protease inhibitor ("Serpin") family, e.g. αl-antitrypsin and antithrombin III. Serpins are regulators of various processes, such as coagulation, inflammatory reactions, complement activation and share a common functional principle and a similar structure, indicative for a common primordial gene. The intron-exon arrangement of Serpin genes may provide a record for the structure of a primordial gene. A comparison of the location of introns among members of the Serpin family reveals that some introns are indeed present at identical or almost identical positions, however in many other cases there is no correspondence between the intron positions among different Serpin genes.Obviously, more data on the chromosomal gene structure of members of this family are required to formulate a scheme for the evolutionary creation of the Serpins. To that end, we have established the number and the precise location of the introns in the PAI-1 gene and have compared these data with those reported on other Serpin genes. For that purpose a human genomic cosmid DNA library of about 340.000 independent colonies was screened with radiolabelled full-length PAI-1 cDNA as probe. Two clones were found which contain the entire PAI-1 gene. Restriction site mapping, electron microscopic inspection of heteroduplexes and nucleotide sequence analysis demonstrate that the PAI-1 gene comprises about 12.2kilo basepairs and consists of nine exons and eight introns. Intron-exon boundaries are all in accord with the "GT-AG" rule, including a cryptic acceptor splice site found in intron 7. Furthermore, it is observed that intron 3 of the PAI-1 gene occupies an identical position as intron E of chicken ovalbumin and intron E of the ovalbumin-related gene Y. The location of the other seven introns is unrelated to the known location of introns in the genes encoding the Serpins, rat angiotensin, chicken ovalbumin (and gene Y), human antithrombin III and human al-antitrypsin. The 3' untranslated region of the PAI-1 gene is devoid of introns, indicating that the two mRNA species detected in cultured endothelial cells which share an identical 5' untranslated segment and codogenic region, but differ in the length of the 3' untranslated region, arise by alternative polyadenylation. An extrapolation of the position of the introns to the amino-acid sequence of PAI-1, and adaption of the view that the subdomain structure of the Serpins is analogous, shows that the introns of PAI-1 are non-randomly distributed. Except for intron 7, the position of the other seven introns corresponds with randon-coil regions of the protein or with the borders of β-sheets and a-helices. Extrapolation of the position of introns in the genes of other Serpins to their respective amino-acid sequences and subdomain structures also reveals a preference for random-coil regions and borders of subdomains. These observations are reminiscent of an evolutionary model, called "intron sliding", that accounts for variations in surface loops of the same protein in different species by aberrant splicing (Craik et al., Science 220 (1983) 1125). The preferential presence of introns in gene segments, encoding these variable regions, and absence in regions determining the general folding of these proteins would explain conservation of the structure during the evolution of those genes.
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Hormann, A., E. J. C. Olson, P. F. Barbara, M. R. Arkin, E. D. A. Stemp, R. E. Holmlin, and J. K. Barton. "Time Resolved Electron Transfer Studies Between Metallointercalators in DNA." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1996. http://dx.doi.org/10.1364/up.1996.sab.6.
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This paper reports the first ultrafast studies on the rates of DNA-mediated forward and reverse electron transfer between photoexcited [M(phen)2dppz]2+ (M=Ru or Os, phen =1,10-phenanthroline, dppz = dipyrido[3,2:a-2′,3′:c]-phenazine) and various electron acceptors in order to ultimately determine the distance dependence of electron transfer kinetics with DNA as an environment.1,2 Previously Barton, Turro, and coworkers have presented evidence that electron transfer in DNA can occur rapidly over an extraordinarily large distance3 with a more shallow distance dependence than that for other media, such as liquids and proteins.4,5 Some theoretical work supports the shallow distance dependence which is attributed to a long range, thermally activated coherent mechanism involving virtual excitation of the DNA "bridge".6 Utilizing time-correlated single photon counting (TCSPC), we observe a substantial fraction of photoexcited [M(phen)2dppz]2+ (M=Ru, Os) exhibits fast oxidative quenching (kq > 3 x 1010 s−1) in the presence of intercalating Rh(III) acceptors while the remaining excited-state species exhibit a range of quenching constants less than 108 s_1. Transient-absorption experiments on the picosecond timescale indicate that, for a series of donors bound to mixed sequence DNA, the majority of back electron transfer is also very fast (ca. 1010 s−1). Importantly, the rate constant for the fast ground-state recovery is independent of loading of Rh(III) intercalators on DNA. As shown in Figure 1, regardless of whether the average loading of metal complexes is 1 in 33 basepairs or 1 in 10 basepairs, the fast bleach recovery exhibited by [Ru(phen)2dppz]2+ is well fit under all conditions by an exponential decay of 9 x 109s−1. Separate ultrafast data suggests that, like the recombination reaction, the fast quenching *M2+ is simple first-order at early time. If the early time electron transfer kinetics were not simple first order, and the electron transfer rate decayed with an exponential distance dependence (i.e. ≅ a factor of 30 per base step [3.4 Å]), our TCSPC apparatus should be able to observe some evidence of the slower components with rate constants in the range of 1010 - 108 s−1. The absence of rates in this range is evidence that the electron transfer is simple first order at time < 10 ns. This result has implications with regards to the donor-acceptor separations on DNA. Throughout most of the titration, intercalators are dilute on the double helix and statistics show that the amount of fast quenching and ground-state recovery observed is too great to be accounted for by random loading of nearest-neighbor pairs. Thus, either the electron transfer reaction must involve clustering of the donor and acceptor on the helix or the DNA-mediated interaction must occur over long distance.
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Henrique Ferreira Cruz, Gustavo, Vinícius Menossi, Josiane Melchiori Pinheiro, Antônio Roberto dos Santos, Gustavo Luiz Furuhata Ferreira, and Sarah Anduca de Oliveira. "Aprendizagem de Máquina na identificação de regiões codantes em sequências de DNA de fungos filamentosos." In Computer on the Beach. Itajaí: Universidade do Vale do Itajaí, 2022. http://dx.doi.org/10.14210/cotb.v13.p236-242.
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The task of identifying intron and exon regions in genes is a verycomplex task, and it is necessary to identify certain nucleotidepatterns in the gene sequence. This task can be done manually orthrough software that most often uses genetic alignment techniques, which is not a very effective way for this purpose. In this oppor-tunity for collaboration between biology and computer science using machine learning techniques, the objective was to predictthe intron and exon regions in filamentous fungi genes as well totranslate the identified regions intro proteic codons. In this paper,the problem was modeled as a supervised learning problem, basedon training a set of genes obtained from GenBank that alreadyhave the intron and exon regions identified. The machine learningmodel used in this work was the Condicional Random Fields (CRF).Through the values resulting from the metrics applied to the model,it can be seen that it is possible to achieve a good precision in thetask of identifying the intron and exon regions as well the proteiccodons. Thus, although there is a need for a greater diversity ofdatabase characteristics to support the effectiveness of identifyingthe splicing sites, this paper gives evidence that it is possible topredict these splicing sites with a good accuracy.
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Korodi, Gergely, and Ioan Tabus. "Random-access compression of annotated DNA sequences." In 2006 IEEE International Workshop on Genomic Signal Processing and Statistics. IEEE, 2006. http://dx.doi.org/10.1109/gensips.2006.353160.
Full textReports on the topic "Random sequence DNA"
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Medrano, Juan, Adam Friedmann, Moshe (Morris) Soller, Ehud Lipkin, and Abraham Korol. High resolution linkage disequilibrium mapping of QTL affecting milk production traits in Israel Holstein dairy cattle. United States Department of Agriculture, March 2008. http://dx.doi.org/10.32747/2008.7696509.bard.
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Original objectives: To create BAC contigs covering two QTL containing chromosomal regions (QTLR) and obtain BAC end sequence information as a platform for SNP identification. Use the SNPs to search for marker-QTL linkage disequilibrium (LD) in the test populations (US and Israel Holstein cattle). Identify candidate genes, test for association with dairy cattle production and functional traits, and confirm any associations in a secondary test population. Revisions in the course of the project: The selective recombinant genotyping (SRG) methodology which we implemented to provide moderate resolution QTL mapping turned out to be less effective than expected, due to problems introduced by incomplete marker informativity. This required a no-cost one-year extension of the project. Aside from this, the project was implemented essentially as envisaged, but only with respect to a single QTLR and single population association-test. Background to the topic. Dairy cattle breeders are looking to marker-assisted selection (MAS) as a means of identifying genetically superior sires and dams. MAS based on population-wide LD can be many times more effective than MAS based on within-family linkage mapping. In this proposal we developed a protocol leading from family based QTL mapping to population-wide LD between markers and the QTL Major conclusions, solutions, achievements. The critical importance of marker informativity for application of the SRG design in outcrossing random mating populations was identified, and an alternative Fractioned Pool Design (FPD) based on selective DNA pooling was developed. We demonstrated the feasibility of constructing a BAC contig across a targeted chromosomal region flanking the marker RM188 on bovine chromosome BTA4, which was shown in previous work to contain a QTL affecting milk production traits. BAC end sequences were obtained and successfully screened for SNPs. LD studies of these SNPs in the Israel population, and of an independent set of SNPs taken across the entire proximal region of BTA4 in the USA population, showed a much lower degree of LD than previously reported in the literature. Only at distances in the sub-cM level did an appreciable fraction of SNP marker-pairs show levels of LD useful for MAS. In contrast, studies in the Israel population using microsatellite markers, presented an equivalent degree of LD at a 1-5 separation distance. SNP LD appeared to reflect historical population size of Bostaurus (Ne=5000- 10,000), while microsatellite LD appeared to be in proportion to more recent effective population size of the Holstein breed (Ne=50-100). An appreciable fraction of the observed LD was due to Family admixture structure of the Holstein population. The SNPs MEOX2/IF2G (found within the gene SETMAR at 23,000 bp from RM188) and SNP23 were significantly associated with PTA protein, Cheese dollars and Net Merit Protein in the Davis bull resource population, and were also associated with protein and casein percentages in the Davis cow resource population. Implications. These studies document a major difference in degree of LD presented by SNPs as compared to microsatellites, and raise questions as to the source of this difference and its implications for QTL mapping and MAS. The study lends significant support to the targeted approach to fine map a previously identified QTL. Using high density genotyping with SNP discovered in flanking genes to the QTL, we have identified important markers associated with milk protein percentage that can be tested in markers assisted selection programs.
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Sadka, Avi, Mikeal L. Roose, and Yair Erner. Molecular Genetic Analysis of Citric Acid Accumulation in Citrus Fruit. United States Department of Agriculture, March 2001. http://dx.doi.org/10.32747/2001.7573071.bard.
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The acid content of the juice sac cells is a major determinant of maturity and fruit quality in citrus. Many citrus varieties accumulate acid in concentrations that exceed market desires, reducing grower income and consumer satisfaction. Pulp acidity is thought to be dependent on two mechanisms: the accumulation of citric acid in the vacuoles of the juice sac cells, and acidification of the vacuole. The major aim of the project was to direct effort toward understanding the mechanism of citric acid accumulation in the fruit. The following objectives were suggested: Measure the activity of enzymes likely to be involved in acid accumulation and follow their pattern of expression in developing fruit (Sadka, Erner). Identify and clone genes which are associated with high and low acid phenotypes and with elevated acid level (Roose, Sadka, Erner). Convert RAPD markers that map near a gene that causes low acid phenotype to specific co dominant markers (Roose). Use genetic co segregation to test whether specific gene products are responsible for low acid phenotype (Roose and Sadka). Objective 1 was fully achieved. Most of the enzymes of organic acid metabolism were cloned from lemon pulp. Their expression was studied during fruit development in low and high acid varieties. The activity and expression of citrate synthase, aconitase and NADP-isocitrate dehydrogenase (IDH) were studied in detail. The role that each enzyme plays in acid accumulation and decline was evaluated. As a result, a better understanding of the metabolic changes that contribute to acid accumulation was achieved. It was found that the activity of the mitochondrial aconitase is greatly reduced early in high-acid fruits, but not in acidless ones, suggesting that this enzyme plays an important role in acid accumulation. In addition, it was demonstrated that increases in the cytosolic forms of aconitase and NADP-IDH towards fruit maturation play probably a major role in acid decline. Our studies also demonstrated that the two mechanisms that contribute to fruit acidity, vacuolar acidification and citric acid accumulation, are independent, although they are tightly co-regulated. Additional, we demonstrated that sodium arsenite, which reduce fruit acidity, causes a transient inhibition in the activity of citrate synthase, but an induction in the gene expression. This part of the work has resulted in 4 papers. Objective 3 was also fully achieved. Using bulked segregant analysis, three random amplified polymorphic DNA (RAPD) markers were identified as linked to acitric, a gene controlling the acidless phenotype of pummelo 2240. One of them, which mapped 1.2 cM from acitric was converted into sequence characterized amplified region (SCAR marker, and into co dominant restriction length polymorphism (RFLP) marker. These markers were highly polymorphic among 59 citrus accessions, and therefore, they should be useful for selecting seedling progeny heterozygous for acitric in nearly all crosses between pummelo 2240 and other citrus genotypes. This part of the project resulted in one paper. Objective 4 was also fully achieved. Clones isolated by the Israeli group were sent to the American laboratory for co segregation analysis. However, none of them seemed to co segregate with the low acid phenotype. Both laboratories invested much effort in achieving the goals of Objective 2, namely the isolation of genes that are elevated in expression in low and high acid phenotypes, and in tissue cultures treated with arsenite (a treatment which reduces fruit acidity). However, conventional differential display and restriction fragment differential display analyses could not identify any differentially expressed genes. The isolation of such genes was the major aim of a continuation project, which was recently submitted.
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Droby, Samir, Joseph W. Eckert, Shulamit Manulis, and Rajesh K. Mehra. Ecology, Population Dynamics and Genetic Diversity of Epiphytic Yeast Antagonists of Postharvest Diseases of Fruits. United States Department of Agriculture, October 1994. http://dx.doi.org/10.32747/1994.7568777.bard.
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One of the emerging technologies is the use of microbial agents for the control of postharvest diseases of fruits and vegetables. A number of antagonistic microorganisms have been discovered which have the potential to effectively control postharvest diseases. Some of this technology has been patented and commercial products such as AspireTM (Ecogen Corporatin, Langhorne, PA, USA), Biosave 10TM and Biosave 11TM (Ecoscience Inc., Worchester, MA, USA) have been registered for commercial use. The principal investigator of this project was involved in developing the yeast-based biofungicide-AspireTM and testing its efficacy under commercial conditions. This research project was initiated to fill the gap between the knowledge available on development and commercial implementation of yeast biocontrol agents and basic understanding of various aspects related to introducing yeast antagonists to fruit surfaces, along with verification of population genetics. The main objectives of this study were: Study ecology, population dynamics and genetic diversity of the yeast antagonists Candida guilliermondii, C. oleophila, and Debaryomyces hansenii, and study the effect of preharvest application of the yeast antagonist C. oleophila naturally occurring epiphytic microbial population and on the development of postharvest diseases of citrus fruit during storage. Our findings, which were detailed in several publications, have shown that an epiphytic yeast population of grapefruit able to grow under high osmotic conditions and a wide range of temperatures was isolated and characterized for its biocontrol activity against green mold decay caused by Penicillium digitatum. Techniques based on random amplified polymorphic DNA (RAPD) and arbitrary primed polymerase chain reaction (ap-PCR), as well as homologies between sequences of the rDNA internal transcribed spacers (ITS) and 5.8S gene, were used to characterize the composition of the yeast population and to determine the genetic relationship among predominant yeast species. Epiphytic yeasts exhibiting the highest biocontrol activity against P. digitatum on grapefruit were identified as Candida guilliermondii, C. oleophila, C. sake, and Debaryomyces hansenii, while C. guilliermondii was the most predominant species. RAPD and ap-PCR analysis of the osmotolerant yeast population showed two different, major groups. The sequences of the ITS regions and the 5.8S gene of the yeast isolates, previously identified as belonging to different species, were found to be identical. Following the need to develop a genetically marked strain of the yeast C. oleophila, to be used in population dynamics studies, a transformation system for the yeast was developed. Histidine auxotrophy of C. oloephila produced using ethyl methanesulfonate were transformed with plasmids containing HIS3, HIS4 and HIS5 genes from Saccharomyces cerevisiae. In one mutant histidin auxotrophy was complemented by the HIS5 gene of S. cerevisiae is functionally homologous to the HIS5 gene in V. oleophila. Southern blot analysis showed that the plasmid containing the S. cerevisiae HIS5 gene was integrated at a different location every C. oleophila HIS+ transformant. There were no detectable physiological differences between C. oleophila strain I-182 and the transformants. The biological control ability of C. oleophila was not affected by the transformation. A genetically marked (with b-glucuronidase gene) transformant of C. oleophila colonized wounds on orange fruits and its population increased under field conditions. Effect of preharvest application of the yeast C. oleophila on population dynamics of epiphytic microbial population on wounded and unwounded grapefruit surface in the orchard and after harvest was also studied. In addition, the effect of preharvest application of the yeast C. oleophila on the development of postharvest decay was evaluated. Population studies conducted in the orchard showed that in control, non-treated fruit, colonization of wounded and unwounded grapefruit surface by naturally occurring filamentous fungi did not vary throughout the incubation period on the tree. On the other hand, colonization of intact and wounded fruit surface by naturally occurring yeasts was different. Yeasts colonized wounded surface rapidly and increased in numbers to about two orders of magnitude as compared to unwounded surface. On fruit treated with the yeast and kept on the tree, a different picture of fungal and yeast population had emerged. The detected fungal population on the yeast-treated intact surface was dramatically reduced and in treated wounds no fungi was detected. Yeast population on intact surface was relatively high immediately after the application of AspireTM and decreased to than 70% of that detected initially. In wounds, yeast population increased from 2.5 x 104 to about 4x106 after 72 hours of incubation at 20oC. Results of tests conducted to evaluate the effect of preharvest application of AspireTM on the development of postharvest decay indicated the validity of the approach.