scholarly journals Deoxyribonucleic acid methylation and chromatin organization in Tetrahymena thermophila.

1981 ◽  
Vol 1 (7) ◽  
pp. 600-608 ◽  
Author(s):  
K Pratt ◽  
S Hattman
Keyword(s):  
Dna Replication ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Cytosine Methylation ◽  
Deoxyribonucleic Acid ◽  
Tetrahymena Thermophila ◽  
Staphylococcal Nuclease ◽  
Chromatin Organization ◽  
Deoxyribonuclease I ◽  
Cell Biol

Deoxyribonucleic acid (DNA) of the transcriptionally active macronucleus of Tetrahymena thermophila is methylated at the N6 position of adenine to produce methyladenine (MeAde); approximately 1 in every 125 adenine residues (0.8 mol%) is methylated. Transcriptionally inert micronuclear DNA is not methylated (< or = 0.01 mol% MeAde; M. A. Gorovsky, S. Hattman, and G. L. Pleger, J. Cell Biol. 56:697-701, 1973). There is no detectable cytosine methylation in macronuclei in Tetrahymena DNA (< or = 0.01 mol% 5-methylcytosine). MeAde-containing DNA sequences in macronuclei are preferentially digested by both staphylococcal nuclease and pancreatic deoxyribonuclease I. In contrast, there is no preferential release of MeAde during digestion of purified DNA. These results indicate that MeAde residues are predominantly located in "linker DNA" and perhaps have a function in transcription. Pulse-chase studies showed that labeled MeAde remains preferentially in linker DNA during subsequent rounds of DNA replication; i.e., there is little, if any, movement of nucleosomes during chromatin replication. This implies that nucleosomes may be phased with respect to DNA sequence.

Deoxyribonucleic acid methylation and chromatin organization in Tetrahymena thermophila

1981 ◽  
Vol 1 (7) ◽  
pp. 600-608
Author(s):  
K Pratt ◽  
S Hattman
Keyword(s):  
Dna Replication ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Cytosine Methylation ◽  
Deoxyribonucleic Acid ◽  
Tetrahymena Thermophila ◽  
Staphylococcal Nuclease ◽  
Chromatin Organization ◽  
Deoxyribonuclease I ◽  
Cell Biol

Deoxyribonucleic acid (DNA) of the transcriptionally active macronucleus of Tetrahymena thermophila is methylated at the N6 position of adenine to produce methyladenine (MeAde); approximately 1 in every 125 adenine residues (0.8 mol%) is methylated. Transcriptionally inert micronuclear DNA is not methylated (< or = 0.01 mol% MeAde; M. A. Gorovsky, S. Hattman, and G. L. Pleger, J. Cell Biol. 56:697-701, 1973). There is no detectable cytosine methylation in macronuclei in Tetrahymena DNA (< or = 0.01 mol% 5-methylcytosine). MeAde-containing DNA sequences in macronuclei are preferentially digested by both staphylococcal nuclease and pancreatic deoxyribonuclease I. In contrast, there is no preferential release of MeAde during digestion of purified DNA. These results indicate that MeAde residues are predominantly located in "linker DNA" and perhaps have a function in transcription. Pulse-chase studies showed that labeled MeAde remains preferentially in linker DNA during subsequent rounds of DNA replication; i.e., there is little, if any, movement of nucleosomes during chromatin replication. This implies that nucleosomes may be phased with respect to DNA sequence.

Scaled Fuzzy Graph for Cluster Analysis in DNA Sequence of Olfactory Receptors

2013 ◽  
Vol 8 (1) ◽  
pp. 57-70
Author(s):  
Satya Ranjan Dash ◽  
Satchidananda Dehuri ◽  
Uma Kant Sahoo
Keyword(s):  
Cluster Analysis ◽  
Dna Sequence ◽  
Simulation Study ◽  
Dna Sequences ◽  
Clustering Algorithm ◽  
Deoxyribonucleic Acid ◽  
Graph Model ◽  
Olfactory Receptors ◽  
Fuzzy Graph ◽  
Before And After

Olfactory receptors (ORs) are responsible for recognition of odor molecules. The deoxyribonucleic acid (DNA) sequences of these receptors are severely affected by local mutations. Therefore, to study the changes among affected and non-affected ORs, the authors attempted to use unsupervised learning (clustering) algorithm. In this paper, they have used a scaled fuzzy graph model for clustering to study the changes before and after the local mutation on DNA sequences of ORs. Their simulation study at the fractional dimensional level confirms its accuracy.

scholarly journals A Color-Image Encryption Scheme Using a 2D Chaotic System and DNA Coding

2019 ◽  
Vol 2019 ◽  
pp. 1-13
Author(s):  
Haidar Raad Shakir
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Deoxyribonucleic Acid ◽  
Color Image ◽  
Color Image Encryption ◽  
Chaotic Sequences ◽  
Xor Operation ◽  
Password Protection ◽  
Differential Attacks ◽  
Exclusive Or

This paper proposes a method of encrypting images with password protection for secure sharing based on deoxyribonucleic acid (DNA) sequence operations and the tangent-delay ellipse reflecting the cavity-map system (TD-ERCS). The initial values of the TD-ERCS system are generated from a user’s password, and the TD-ERCS system is used to scramble the pixel locations of the R, G, and B matrices of the original image. Next, three DNA-sequence matrices are generated by encoding the permuted color image such that it can be transformed into three matrices. Then, the TD-ERCS system is employed to generate three chaotic sequences before encoding the DNA into the three matrices. Thereafter, a DNA exclusive OR (XOR) operation is executed between the DNA sequences of the permuted image and the DNA sequences generated by the TD-ERCS system to produce three encrypted scrambled matrices. Finally, the matrices of the DNA sequences are decoded, and the R, G, and B channels are recombined to form an encrypted color image. The results of simulation and security tests reveal that the proposed algorithm offers robust encryption and demonstrates the ability to resist exhaustive, statistical, and differential attacks.

scholarly journals Absence of MeCP2 binding to non-methylated GT-rich sequences in vivo

2020 ◽  
Vol 48 (7) ◽  
pp. 3542-3552 ◽  
Author(s):  
John C Connelly ◽  
Justyna Cholewa-Waclaw ◽  
Shaun Webb ◽  
Verdiana Steccanella ◽  
Bartlomiej Waclaw ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Cytosine Methylation ◽  
Epigenetic Mark ◽  
Primary Role ◽  
Flanking Sequence ◽  
Primary Determinant ◽  
Human Neuronal Cells

Abstract MeCP2 is a nuclear protein that binds to sites of cytosine methylation in the genome. While most evidence confirms this epigenetic mark as the primary determinant of DNA binding, MeCP2 is also reported to have an affinity for non-methylated DNA sequences. Here we investigated the molecular basis and in vivo significance of its reported affinity for non-methylated GT-rich sequences. We confirmed this interaction with isolated domains of MeCP2 in vitro and defined a minimal target DNA sequence. Binding depends on pyrimidine 5′ methyl groups provided by thymine and requires adjacent guanines and a correctly orientated A/T-rich flanking sequence. Unexpectedly, full-length MeCP2 protein failed to bind GT-rich sequences in vitro. To test for MeCP2 binding to these motifs in vivo, we analysed human neuronal cells using ChIP-seq and ATAC-seq technologies. While both methods robustly detected DNA methylation-dependent binding of MeCP2 to mCG and mCAC, neither showed evidence of MeCP2 binding to GT-rich motifs. The data suggest that GT binding is an in vitro phenomenon without in vivo relevance. Our findings argue that MeCP2 does not read unadorned DNA sequence and therefore support the notion that its primary role is to interpret epigenetic modifications of DNA.

scholarly journals The self-similarity properties and multifractal analysis of DNA sequences

2019 ◽  
Vol 4 (1) ◽  
pp. 267-278 ◽  
Author(s):  
G. Durán-Meza ◽  
J. López-García ◽  
J.L. del Río-Correa
Keyword(s):  
Hausdorff Dimension ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Multifractal Analysis ◽  
Deoxyribonucleic Acid ◽  
Point Of View ◽  
The Self ◽  
Hölder Exponent ◽  
Self Similarity ◽  
Multifractal Decomposition

AbstractIn this work is presented a pedagogical point of view of multifractal analysis deoxyribonucleic acid (DNA) sequences is presented. The DNA sequences are formed by 4 nucleotides (adenine, cytosine, guanine, and tymine). Following Jeffrey’s paper we associated a simple contractive function to each nucleotide, and constructed the Hutchinson’s operator W, which was used to build covers of different sizes of the unitary square Q, thus Wk(Q) is a cover of Q, conformed by 4k squares Qk of size 2−k, as each Qk corresponds to a unique subsequence of nucleotides with length k : b1b2...bk. Besides, it is obtained the optimal cover Ck to the fractal F generated for each DNA sequence was obtained. We made a multifractal decomposition of Ck in terms of the sets Jα conformed by the Qk’s with the same value of the Holder exponent α, and determined f (α), the Hausdorff dimension of Jα, using the curdling theorem.

FPGA Based Data Hiding Methods using DNA Cryptography Techniques

2016 ◽  
Vol 5 (3) ◽  
pp. 141
Author(s):  
B. Murali Krishna ◽  
CH. Surendra ◽  
K. Mani Varma ◽  
K. Mani Kanta ◽  
S.K. Shabbeer ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Deoxyribonucleic Acid ◽  
Specific Reference ◽  
Insertion Technique ◽  
Second Stage ◽  
Dna Cryptography ◽  
Single Strategy ◽  
Security Algorithm ◽  
Two Stages

<p>To convey the information safely DNA grouping mechanisms are used. There are many methods used by DNA sequences. The proposed method is of both encryption and information concealing utilizing a few properties of Deoxyribonucleic Acid (DNA) groupings. This technique is highlighted that DNA groupings have many more intriguing properties which are used for concealing the information. There are three strategies in this encryption strategy: the Insertion Technique, the Complimentary Pair Technique and the Substitution Strategy .For every single strategy, a specific reference DNA grouping P is chosen and then the taken sequence is changed over with the mystery message M and is consolidated, so that P0 is acquired. P0 is then sent to the collector and the beneficiary can recognize and separate the message M covered up in P. This technique is proposed to utilize INSERTION Strategy. Subsequently, the proposed plan comprises for the most part of two stages. In the principal stage, the mystery information is encoded utilizing a DNA Sequence. In the second stage the encoded information is steganographically covered up into some reference DNA grouping utilizing an insertion strategy. The effectiveness of this security algorithm is seen with many merits and limitations. A, C, G, and T are the 4 nucleotides which are taken for this project.</p>

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

scholarly journals DNA thermodynamics shape chromosome organization and topology

2013 ◽  
Vol 41 (2) ◽  
pp. 548-553 ◽  
Author(s):  
Andrew A. Travers ◽  
Georgi Muskhelishvili
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Chromosome Organization ◽  
Topological Properties ◽  
Genetic Organization ◽  
And Topology ◽  
Dna Translocases

How much information is encoded in the DNA sequence of an organism? We argue that the informational, mechanical and topological properties of DNA are interdependent and act together to specify the primary characteristics of genetic organization and chromatin structures. Superhelicity generated in vivo, in part by the action of DNA translocases, can be transmitted to topologically sensitive regions encoded by less stable DNA sequences.

scholarly journals An application of slow feature analysis to the genetic sequences of coronaviruses and influenza viruses

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Anastasios A. Tsonis ◽  
Geli Wang ◽  
Lvyi Zhang ◽  
Wenxu Lu ◽  
Aristotle Kayafas ◽  
...  
Keyword(s):  
Mathematical Method ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Transmission Rate ◽  
Complex Structure ◽  
Mortality Rates ◽  
Influenza Viruses ◽  
Feature Analysis ◽  
Slow Feature Analysis ◽  
Genetic Sequences

Abstract Background Mathematical approaches have been for decades used to probe the structure of DNA sequences. This has led to the development of Bioinformatics. In this exploratory work, a novel mathematical method is applied to probe the DNA structure of two related viral families: those of coronaviruses and those of influenza viruses. The coronaviruses are SARS-CoV-2, SARS-CoV-1, and MERS. The influenza viruses include H1N1-1918, H1N1-2009, H2N2-1957, and H3N2-1968. Methods The mathematical method used is the slow feature analysis (SFA), a rather new but promising method to delineate complex structure in DNA sequences. Results The analysis indicates that the DNA sequences exhibit an elaborate and convoluted structure akin to complex networks. We define a measure of complexity and show that each DNA sequence exhibits a certain degree of complexity within itself, while at the same time there exists complex inter-relationships between the sequences within a family and between the two families. From these relationships, we find evidence, especially for the coronavirus family, that increasing complexity in a sequence is associated with higher transmission rate but with lower mortality. Conclusions The complexity measure defined here may hold a promise and could become a useful tool in the prediction of transmission and mortality rates in future new viral strains.

Micronuclear DNA sequences from Tetrahymena do not confer mitotic stability on ARS plasmids in Saccharomyces

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 690-696 ◽  
Author(s):  
Wendy H. Horsfall ◽  
Ronald E. Pearlman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Sequences ◽  
Copy Number ◽  
Tetrahymena Thermophila ◽  
Assay System ◽  
Mitotic Stability ◽  
Yeast Saccharomyces Cerevisiae ◽  
Genomic Libraries ◽  
Ade2 Gene

Genomic libraries containing micronuclear DNA sequences from Tetrahymena thermophila have been constructed in a vector containing ARS1, SUP11, and ura3 sequences from the yeast Saccharomyces cerevisiae. When transformed into a strain of S. cerevisiae carrying a suppressible ochre mutation in the ade2 gene, viable transformants are obtained only if the transforming plasmid is maintained at a copy number of one or two per cell. Mitotic segregation of the plasmid is easily assessed in a colour assay of transformants. Using this assay system, we showed that micronuclear DNA from Tetrahymena does not contain sequences that confer mitotic stability on yeast ARS-containing plasmids; i.e., sequences that function analogously to yeast centromere sequences. One transformant was analyzed that carries Tetrahymena sequences that maintain the copy number of the ARS plasmid at one or two per cell. However, these sequences do not confer mitotic stability on the transformants and they confer a phenotype in this assay similar to that of the REP3 gene of the yeast 2 μm plasmid.Key words: mitotic stability, centromere, Tetrahymena, Saccharomyces.

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