scholarly journals Patterns of Ancestral Human Diversity: An Analysis of Alu-Insertion and Restriction-Site Polymorphisms

2001 ◽  
Vol 68 (3) ◽  
pp. 738-752 ◽  
Author(s):  
W.S. Watkins ◽  
C.E. Ricker ◽  
M.J. Bamshad ◽  
M.L. Carroll ◽  
S.V. Nguyen ◽  
...  
Keyword(s):  
Restriction Site ◽  
Human Diversity ◽  
Alu Insertion ◽  
Restriction Site Polymorphisms

scholarly journals Species ofBorreliadistinguished by restriction site polymorphisms in 16S rRNA genes

1993 ◽  
Vol 111 (2-3) ◽  
pp. 239-243 ◽  
Author(s):  
David Ralph ◽  
Daniele Postic ◽  
Guy Baranton ◽  
Charles Pretzman ◽  
Michael McClelland
Keyword(s):  
16S Rrna ◽  
Restriction Site ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Restriction Site Polymorphisms

Assignment of two mitochondrially synthesized polypeptides to human mitochondrial DNA and their use in the study of intracellular mitochondrial interaction

1982 ◽  
Vol 2 (1) ◽  
pp. 30-41
Author(s):  
N A Oliver ◽  
D C Wallace
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Site ◽  
Mitochondrial Protein ◽  
Mitochondrial Protein Synthesis ◽  
Human Mitochondrial Dna ◽  
Ht1080 Cells ◽  
Mitochondrial Dnas ◽  
A Cell ◽  
Dna Restriction ◽  
Restriction Site Polymorphisms

Two mitochondrially synthesized marker polypeptides, MV-1 and MV-2, were found in human HeLa and HT1080 cells. These were assigned to the mitochondrial DNA in HeLa-HT1080 cybrids and hybrids by demonstrating their linkage to cytoplasmic genetic markers. These markers include mitochondrial DNA restriction site polymorphisms and resistance to chloramphenicol, an inhibitor of mitochondrial protein synthesis. In the absence of chloramphenicol, the expression of MV-1 and MV-2 in cybrids and hybrids was found to be directly proportional to the ratio of the parental mitochondrial DNAs. In the presence of chloramphenicol, the marker polypeptide linked to the chloramphenicol-sensitive mitochondrial DNA continued to be expressed. This demonstrated that resistant and sensitive mitochondrial DNAs can cooperate within a cell for gene expression and that the CAP-resistant allele was dominant or codominant to sensitive. Such cooperation suggests that mitochondrial DNAs can be exchanged between mitochondria.

scholarly journals Chromosomal mapping of murine c-fes and c-src genes.

1984 ◽  
Vol 4 (5) ◽  
pp. 978-981 ◽  
Author(s):  
C Blatt ◽  
M E Harper ◽  
G Franchini ◽  
M N Nesbitt ◽  
M I Simon
Keyword(s):  
Kinase Activity ◽  
Restriction Site ◽  
Mouse Genome ◽  
Inbred Strains ◽  
Chromosomal Mapping ◽  
Chromosome 2 ◽  
Distal Half ◽  
Viral Oncogenes ◽  
Tyrosine Specific Kinase ◽  
Restriction Site Polymorphisms

The murine homologs of two viral oncogenes associated with tyrosine-specific kinase activity have been assigned to different loci in the mouse genome. The segregation of restriction site polymorphisms, as detected by probes that are specific for endogenous c-fes and c-src sequences, was followed in the DNA of recombinant inbred strains. The c-fes gene was mapped to the proximal portion of chromosome 7, very close to the Gpi-1 locus, whereas c-src was linked to the Psp locus on the distal half of chromosome 2.

scholarly journals Variegated phenotype and developmental methylation changes of a maize allele originating from epimutation.

Genetics ◽  
1994 ◽  
Vol 136 (3) ◽  
pp. 1121-1141 ◽  
Author(s):  
O P Das ◽  
J Messing
Keyword(s):  
Tissue Specificity ◽  
Restriction Site ◽  
Genomic Analysis ◽  
Epigenetic Mechanism ◽  
Transcript Levels ◽  
Genetic Transmission ◽  
Cell Divisions ◽  
P Gene ◽  
Expression Potential ◽  
Restriction Site Polymorphisms

Abstract Two instances of genetic transmission of spontaneous epimutation of the maize P-rr gene were identified. Transmission gave rise to two similar, moderately stable alleles, designated P-pr-1 and P-pr-2, that exhibited Mendelian behavior. Both isolates of P-pr conditioned a variable and variegated phenotype, unlike the uniform pigmentation conditioned by P-rr. Extensive genomic analysis failed to reveal insertions, deletions or restriction site polymorphisms between the new allele and its progenitor. However, methylation of the P gene was increased in P-pr relative to P-rr, and was greatly reduced (though not lost) in a revertant to uniform pigmentation. Variability in pigmentation conditioned by P-pr correlated with variability in transcript levels of the P gene, and both correlated inversely with variability in its methylation. Part of the variability in methylation could be accounted for by a developmental decrease in methylation in all tissues of plants carrying P-pr. We hypothesize that the variegated phenotype results from a general epigenetic pathway which causes a progressive decrease in methylation and increase in expression potential of the P gene as a function of cell divisions in each meristem of the plant. This renders all tissues chimeric for a functional gene; chimerism is visualized as variegation only in pericarp due to the tissue specificity of P gene expression. Therefore, this allele that originates from epimutation may exemplify an epigenetic mechanism for variegation in maize.

scholarly journals Analysis of a circular derivative of Saccharomyces cerevisiae chromosome III: a physical map and identification and location of ARS elements.

Genetics ◽  
1991 ◽  
Vol 129 (2) ◽  
pp. 343-357 ◽  
Author(s):  
C S Newlon ◽  
L R Lipchitz ◽  
I Collins ◽  
A Deshpande ◽  
R J Devenish ◽  
...  
Keyword(s):  
High Frequency ◽  
Restriction Site ◽  
Physical Map ◽  
Recombination Rates ◽  
Recombinant Plasmids ◽  
Ars Elements ◽  
Physical Maps ◽  
Chromosome Iii ◽  
High Frequency Transformation ◽  
Restriction Site Polymorphisms

Abstract DNA was isolated from a circular derivative of chromosome III to prepare a library of recombinant plasmids enriched in chromosome III sequences. An ordered set of recombinant plasmids and bacteriophages carrying the contiguous 210-kilobase region of chromosome III between the HML and MAT loci was identified, and a complete restriction map was prepared with BamHI and EcoRI. Using the high frequency transformation assay and extensive subcloning, 13 ARS elements were mapped in the cloned region. Comparison of the physical maps of chromosome III from three strains revealed that the chromosomes differ in the number and positions of Ty elements and also show restriction site polymorphisms. A comparison of the physical map with the genetic map shows that meiotic recombination rates vary at least tenfold along the length of the chromosome.

scholarly journals GBStools: A Unified Approach for Reduced Representation Sequencing and Genotyping

2015 ◽  
Author(s):  
Thomas F Cooke ◽  
Muh-Ching Yee ◽  
Marina Muzzio ◽  
Alexandra Sockell ◽  
Ryan Bell ◽  
...  
Keyword(s):  
Restriction Site ◽  
Variant Calling ◽  
Simulated Data ◽  
Error Rates ◽  
Genomic Diversity ◽  
Model Organisms ◽  
Data Sets ◽  
Reduced Representation ◽  
Restriction Site Polymorphisms ◽  
Reduced Representation Sequencing

Reduced representation sequencing methods such as genotyping-by-sequencing (GBS) enable low-cost measurement of genetic variation without the need for a reference genome assembly. These methods are widely used in genetic mapping and population genetics studies, especially with non-model organisms. Variant calling error rates, however, are higher in GBS than in standard sequencing, in particular due to restriction site polymorphisms, and few computational tools exist that specifically model and correct these errors. We developed a statistical method to remove errors caused by restriction site polymorphisms, implemented in the software package GBStools. We evaluated it in several simulated data sets, varying in number of samples, mean coverage and population mutation rate, and in two empirical human data sets (N = 8 and N = 63 samples). In our simulations, GBStools improved genotype accuracy more than commonly used filters such as Hardy-Weinberg equilibrium p-values. GBStools is most effective at removing genotype errors in data sets over 100 samples when coverage is 40X or higher, and the improvement is most pronounced in species with high genomic diversity. We also demonstrate the utility of GBS and GBStools for human population genetic inference in Argentine populations and reveal widely varying individual ancestry proportions and an excess of singletons, consistent with recent population growth.

scholarly journals Meiotic instability of the R-r complex arising from displaced intragenic exchange and intrachromosomal rearrangement.

Genetics ◽  
1991 ◽  
Vol 129 (1) ◽  
pp. 271-283 ◽  
Author(s):  
T P Robbins ◽  
E L Walker ◽  
J L Kermicle ◽  
M Alleman ◽  
S L Dellaporta
Keyword(s):  
Biosynthetic Pathway ◽  
Restriction Site ◽  
Single Gene ◽  
Intragenic Recombination ◽  
R Genes ◽  
Anthocyanin Pigment ◽  
P Gene ◽  
Intrachromosomal Rearrangement ◽  
Or Gene ◽  
Restriction Site Polymorphisms

Abstract The R complex of Zea mays encodes a tissue-specific transcriptional activator of the anthocyanin pigment biosynthetic pathway. Certain R alleles comprise two genetically distinct components that confer the plant (P) and seed (S) aspects of the pigmentation pattern. These alleles are meiotically unstable, losing (P) or (S) function, often accompanied by exchange of flanking markers. We show that the (P) component consists of a single gene within the R-r complex, whereas the (S) component is part of a more complex arrangement of multiple R genes or gene subfragments. A third, cryptic region of the complex, termed (Q), consists of a truncated R sequence. The analysis of R-r crossover derivative alleles shows they arise from unequal exchange between the (P) gene and one of several distinct regions of the R-r complex. Restriction site polymorphisms were used to show that most of these unequal exchanges are intragenic. The frequency of displaced intragenic recombination is comparable to previous estimates for intragenic recombination in maize involving genes that are not duplicated. These exchange events have been used to determine the arrangement of components within the complex and their orientation in the chromosome. We also show that localized rearrangements in the (P) or (S) components are responsible for noncrossover derivative alleles. The organization of R-r has implications for these noncrossover derivatives and models for their origin are discussed.

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