scholarly journals DNA Sequence Analyses Support the Role of Interrupted Gap Repair in the Origin of Internal Deletions of the Maize Transposon, MuDR

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 603-618 ◽  
Author(s):  
An-Ping Hsia ◽  
Patrick S Schnable
Keyword(s):  
Dna Sequence ◽  
Physical Mapping ◽  
Dna Sequences ◽  
Coding Region ◽  
Sequence Analyses ◽  
Break Points ◽  
The Relationship ◽  
Derivatives Of

Abstract Previous research has demonstrated that the autonomous Cy transposon can activate the excision of Mu transposons. To determine the relationship between Cy and the more recently described autonomous Mu transposon, MuDR, a Cy transposon inserted at the mutable a1 allele, a1-m5216, was isolated and cloned. DNA sequence analyses established that this Cy insertion is identical to MuDR (Mu9, GenBank accession No.: m76978.gb_pl). Therefore, Cy will henceforth be termed MuDR:Cy. Defective derivatives of MuDR:Cy were isolated that had lost their capacity to activate their own excision or the excision of a Mu7 transposon. Most of these derivatives are nonautonomous transposons because they can excise, but only in the presence of unlinked MuDR:Cy transposons. Physical mapping and DNA sequence analyses have established that six of these defective derivatives carry internal deletions. It has been proposed previously that such deletions arise via interrupted gap repair. The DNA sequences of the break points associated with all four sequenced deletions are consistent with this model. The finding that three of the excision-defective derivatives carry deletions that disrupt the coding region of the mudrA (but not the mudrB) transcript supports the view that mudrA plays a role in the excision of Mu transposons.

scholarly journals Structural defects of a Pax8 mutant that give rise to congenital hypothyroidism

1999 ◽  
Vol 341 (1) ◽  
pp. 89-93 ◽  
Author(s):  
Gianluca TELL ◽  
Lucia PELLIZZARI ◽  
Gennaro ESPOSITO ◽  
Carlo PUCILLO ◽  
Paolo Emidio MACCHIA ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Congenital Hypothyroidism ◽  
Dna Sequences ◽  
Dna Interaction ◽  
Structural Defects ◽  
Molecular Defect ◽  
Wild Type ◽  
Coding Region ◽  
Induced Fit ◽  
Helical Content

Pax proteins are transcriptional regulators that play important roles during embryogenesis. These proteins recognize specific DNA sequences via a conserved element: the paired domain (Prd domain). The low level of organized secondary structure, in the free state, is a general feature of Prd domains; however, these proteins undergo a dramatic gain in α-helical content upon interaction with DNA (‘induced fit’). Pax8 is expressed in the developing thyroid, kidney and several areas of the central nervous system. In humans, mutations of the Pax8 gene, which are mapped to the coding region of the Prd domain, give rise to congenital hypothyroidism. Here, we have investigated the molecular defects caused by a mutation in which leucine at position 62 is substituted for an arginine. Leu62 is conserved among Prd domains, and contributes towards the packing together of helices 1 and 3. The binding affinity of the Leu62Arg mutant for a specific DNA sequence (the C sequence of thyroglobulin promoter) is decreased 60-fold with respect to the wild-type Pax8 Prd domain. However, the affinities with which the wild-type and the mutant proteins bind to a non-specific DNA sequence are very similar. CD spectra demonstrate that, in the absence of DNA, both wild-type Pax8 and the Leu62Arg mutant possess a low α-helical content; however, in the Leu62Arg mutant, the gain in α-helical content upon interaction with DNA is greatly reduced with respect to the wild-type protein. Thus the molecular defect of the Leu62Arg mutant causes a reduced capability for induced fit upon DNA interaction.

Multi-Fractal Analysis for Feature Extraction from DNA Sequences

2012 ◽  
pp. 100-118
Author(s):  
Witold Kinsner ◽  
Hong Zhang
Keyword(s):  
Feature Extraction ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Window Size ◽  
Signal Spectrum ◽  
Coding Region ◽  
Lévy Walk ◽  
Fractal Measures ◽  
Levy Walk ◽  
Biological Functionality

This paper presents estimations of multi-scale (multi-fractal) measures for feature extraction from deoxyribonucleic acid (DNA) sequences, and demonstrates the intriguing possibility of identifying biological functionality using information contained within the DNA sequence. We have developed a technique that seeks patterns or correlations in the DNA sequence at a higher level than the local base-pair structure. The technique has three main steps: (i) transforms the DNA sequence symbols into a modified Lévy walk, (ii) transforms the Lévy walk into a signal spectrum, and (iii) breaks the spectrum into sub-spectra and treats each of these as an attractor from which the multi-fractal dimension spectrum is estimated. An optimal minimum window size and volume element size are found for estimation of the multi-fractal measures. Experimental results show that DNA is multi-fractal, and that the multi-fractality changes depending upon the location (coding or non-coding region) in the sequence.

scholarly journals Relationship between DNA polymorphism and fixation time.

Genetics ◽  
1990 ◽  
Vol 125 (2) ◽  
pp. 447-454 ◽  
Author(s):  
F Tajima
Keyword(s):  
Computer Simulation ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dna Polymorphism ◽  
Random Mating ◽  
Random Time ◽  
Fixation Time ◽  
Expected Number ◽  
Mating Population ◽  
The Relationship

Abstract When there is no recombination among nucleotide sites in DNA sequences, DNA polymorphism and fixation of mutants at nucleotide sites are mutually related. Using the method of gene genealogy, the relationship between the DNA polymorphism and the fixation of mutant nucleotide was quantitatively investigated under the assumption that mutants are selectively neutral, that there is no recombination among nucleotide sites, and that the population is a random mating population with N diploid individuals. The results obtained indicate that the expected number of nucleotide differences between two DNA sequences randomly sampled from the population is 42% less when a mutant at a particular nucleotide site reaches fixation than at a random time, and that heterozygosity is also expected to be less when fixation takes place than at a random time, but the amount of reduction depends on the value of 4Nv in this case, where v is the mutation rate per DNA sequence per generation. The formula for obtaining the expected number of nucleotide differences between the two DNA sequences for a given fixation time is also derived, and indicates that, even when it takes a large number of generations for a mutant to reach fixation, this number is 33% less than at a random time. The computer simulation conducted suggests that the expected number of nucleotide differences between the two DNA sequences at the time when an advantageous mutant becomes fixed is essentially the same as that of neutral mutant if the fixation time is the same. The effect of recombination on the amount of DNA polymorphism was also investigated by using computer simulation.

scholarly journals DNA sequence of two linked actin genes of sea urchin.

1983 ◽  
Vol 3 (3) ◽  
pp. 448-456 ◽  
Author(s):  
M A Schuler ◽  
P McOsker ◽  
E B Keller
Keyword(s):  
Amino Acids ◽  
Dna Sequence ◽  
Sea Urchin ◽  
Dna Sequences ◽  
Coding Region ◽  
Slime Molds ◽  
Tandem Gene Duplication ◽  
Coding Regions ◽  
Actin Genes ◽  
Cytoplasmic Actin

DNA sequences have been determined for two actin genes which are closely linked in the genome of the sea urchin Strongylocentrotus purpuratus. The two genes have the same 5'-3' orientation; they were apparently formed originally by tandem gene duplication. The amino acids encoded by the two genes closely resemble those of cytoplasmic actins of mammals and slime molds and differ somewhat from those of mammalian muscle actin. Actin gene 1 had been tentatively identified earlier as the gene for an embryonic cytoplasmic actin by the homology of the 3' noncoding region with that of the cDNA of an embryonic actin mRNA from S. purpuratus. The DNA sequence of gene 1 shows presumptive signals for the initiation and termination of transcription which would govern the formation of a mature mRNA of 1.9 kilobases. Both actin genes 1 and 2 have introns in their coding regions at codons 121/122 and 204. These positions for actin introns have been reported so far only in the rat, not in lower organisms. The divergence of the sequences of these coding-region introns in the two actin genes is 66%, suggesting that the genes diverged about 90 million years ago. By contrast to the introns, the coding regions have been highly conserved; the amino acids of the two genes differ by only 1.3%, and the silent sites of the codons differ by only 12%.

scholarly journals “Cumulative Stress”: The Effects of Maternal and Neonatal Oxidative Stress and Oxidative Stress-Inducible Genes on Programming of Atopy

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Sara Manti ◽  
Lucia Marseglia ◽  
Gabriella D’Angelo ◽  
Caterina Cuppari ◽  
Erika Cusumano ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Dna Sequences ◽  
Allergic Diseases ◽  
Atopic Diseases ◽  
Cumulative Stress ◽  
Inducible Genes ◽  
The Relationship ◽  
And Oxidative Stress ◽  
Epigenetic Pattern

Although extensive epidemiological and laboratory studies have been performed to identify the environmental and immunological causes of atopy, genetic predisposition seems to be the biggest risk factor for allergic diseases. The onset of atopic diseases may be the result of heritable changes of gene expression, without any alteration in DNA sequences occurring in response to early environmental stimuli. Findings suggest that the establishment of a peculiar epigenetic pattern may also be generated by oxidative stress (OS) and perpetuated by the activation of OS-related genes. Analyzing the role of maternal and neonatal oxidative stress and oxidative stress-inducible genes, the purpose of this review was to summarize what is known about the relationship between maternal and neonatal OS-related genes and the development of atopic diseases.

Multi-Fractal Analysis for Feature Extraction from DNA Sequences

2010 ◽  
Vol 2 (2) ◽  
pp. 1-18 ◽  
Author(s):  
Witold Kinsner ◽  
Hong Zhang
Keyword(s):  
Feature Extraction ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Window Size ◽  
Signal Spectrum ◽  
Coding Region ◽  
Lévy Walk ◽  
Fractal Measures ◽  
Levy Walk ◽  
Biological Functionality

This paper presents estimations of multi-scale (multi-fractal) measures for feature extraction from deoxyribonucleic acid (DNA) sequences, and demonstrates the intriguing possibility of identifying biological functionality using information contained within the DNA sequence. We have developed a technique that seeks patterns or correlations in the DNA sequence at a higher level than the local base-pair structure. The technique has three main steps: (i) transforms the DNA sequence symbols into a modified Lévy walk, (ii) transforms the Lévy walk into a signal spectrum, and (iii) breaks the spectrum into sub-spectra and treats each of these as an attractor from which the multi-fractal dimension spectrum is estimated. An optimal minimum window size and volume element size are found for estimation of the multi-fractal measures. Experimental results show that DNA is multi-fractal, and that the multi-fractality changes depending upon the location (coding or non-coding region) in the sequence.

The Corporeal Stenographer: Language, Gesture, and Cyberspace

Leonardo ◽  
1999 ◽  
Vol 32 (5) ◽  
pp. 383-389
Author(s):  
Tiffany Holmes
Keyword(s):  
Medical Imaging ◽  
Dna Sequences ◽  
Scientific Literacy ◽  
The Body ◽  
Imaging Technologies ◽  
Creative Practice ◽  
The Relationship

The author describes her research and creative practice exploring the intersection between digital, biomedical, and linguistic modes of bodi ly representation. She synthesizes traditional forms of painting with new computer and medical imaging technologies to call into question the relationship between visible and invisible bodily forms and actions. Her paintings and installations use scientifically rendered images of the body (from symbolic DNA sequences to developing cel lular structures) in order to consider the role of the tools and technologies used to organize and view these images. The issue of visual, linguistic, and scientific literacy is thus a corollary concern.

scholarly journals Genetic structure and DNA sequences at junctions involved in the rearrangements of Bacillus subtilis strains carrying the trpE26 mutation.

Genetics ◽  
1990 ◽  
Vol 126 (4) ◽  
pp. 785-797 ◽  
Author(s):  
E D Jarvis ◽  
S Cheng ◽  
R Rudner
Keyword(s):  
Bacillus Subtilis ◽  
Dna Sequences ◽  
Restriction Site ◽  
Physical Analysis ◽  
Area 5 ◽  
Ribosomal Operon ◽  
Break Points ◽  
Type Strains

Abstract Studies on the region upstream to ribosomal operon rrnD of Bacillus subtilis led to the characterization of two of the four chromosomal junctions involved in the rearrangements (a translocation and an inversion) of the strains carrying the trpE26 mutation. Genetic analysis, by integrative mapping, showed linkage of rrnD to cysB and hisA (both on segment A) in the trpE26-type strains. Physical analysis showed that the region upstream to rrnD is now linked to the trpE-ilvA chromosome segment as demonstrated by analyzing restriction site-polymorphism between 168 and trpE26-type strains. Similar experiments confirmed the previous genetic data on linkage in these areas in strains carrying novel rearrangements derived from the trpE26-type strains: stable merodiploids and inversions. The nucleotide sequence of the area 5' to rrnD in both types of strains (168 and trpE26), the region downstream of the citG gene and the region carrying the trpE26 mutation (made available to us by D. Henner) provided evidence for the molecular basis of the differences in structure, allowed the identification of the break points and revealed the presence of a polypurine region upstream to rrnD as seen in other systems in B. subtilis. No extensive homology was found between pairs of junctions so far sequenced. The models proposed by C. Anagnostopoulos for the role of DNA sequences of intrachromosomal homology involved in the transfer of the trpE26 mutation and the formation of novel arrangements require therefore reevaluation.

DNA sequence of two linked actin genes of sea urchin

1983 ◽  
Vol 3 (3) ◽  
pp. 448-456
Author(s):  
M A Schuler ◽  
P McOsker ◽  
E B Keller
Keyword(s):  
Amino Acids ◽  
Dna Sequence ◽  
Sea Urchin ◽  
Dna Sequences ◽  
Coding Region ◽  
Slime Molds ◽  
Tandem Gene Duplication ◽  
Coding Regions ◽  
Actin Genes ◽  
Cytoplasmic Actin

DNA sequences have been determined for two actin genes which are closely linked in the genome of the sea urchin Strongylocentrotus purpuratus. The two genes have the same 5'-3' orientation; they were apparently formed originally by tandem gene duplication. The amino acids encoded by the two genes closely resemble those of cytoplasmic actins of mammals and slime molds and differ somewhat from those of mammalian muscle actin. Actin gene 1 had been tentatively identified earlier as the gene for an embryonic cytoplasmic actin by the homology of the 3' noncoding region with that of the cDNA of an embryonic actin mRNA from S. purpuratus. The DNA sequence of gene 1 shows presumptive signals for the initiation and termination of transcription which would govern the formation of a mature mRNA of 1.9 kilobases. Both actin genes 1 and 2 have introns in their coding regions at codons 121/122 and 204. These positions for actin introns have been reported so far only in the rat, not in lower organisms. The divergence of the sequences of these coding-region introns in the two actin genes is 66%, suggesting that the genes diverged about 90 million years ago. By contrast to the introns, the coding regions have been highly conserved; the amino acids of the two genes differ by only 1.3%, and the silent sites of the codons differ by only 12%.

The Length Design of the Same Largest Subsequence

2013 ◽  
Vol 420 ◽  
pp. 343-345 ◽  
Author(s):  
Fang Fang Ma ◽  
Han Li
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
False Positive ◽  
Basic Problem ◽  
Dna Encoding ◽  
Dna Computation ◽  
Sequence Design ◽  
Dna Sequence Design ◽  
The Relationship

DNA sequence design which is also called DNA encoding is a basic problem in DNA computation. The strands involved in the experiments should not exhibit any undesired behavior, especially they should not form false positive. So they could ensure the efficiency and veracity of the experiments. The properties of subsequences can reflect those of the whole DNA sequences. The definitions of the same subsequence and the same largest subsequence are proposed in this paper. And the relationship between them can be got. By analyzing properties of the same largest subsequence, the length can be achieved.

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