DNA sequence of a small, unidentified plasmid isolated from a Haemophilus somnus strain: Short communication

2001 ◽  
Vol 49 (1) ◽  
pp. 11-16 ◽  
Author(s):  
R. Izadpanah ◽  
Á. Dán ◽  
Mária Benkő ◽  
M. Rusvai ◽  
L. Fodor ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Respiratory Disease ◽  
Dna Sequence ◽  
Short Communication ◽  
Nasal Discharge ◽  
Base Pairs ◽  
Haemophilus Somnus ◽  
Specific Factors

One of the plasmids present in a Haemophilus somnus strain isolated from nasal discharge of a cattle with respiratory disease was purified and cloned for DNA sequencing. The plasmid was found to be 1065 base pairs long with 39.2% G+C content, and showed no homology to any DNA sequenced so far. It has no capacity to code any protein longer than 43 residues. It is not clear yet if this plasmid codes Haemophilus somnus specific factors.

DNA sequence of a small, unidentified plasmid isolated from a Haemophilus somnus strain: Short communication

2001 ◽  
Vol 49 (1) ◽  
pp. 11-16 ◽  
Author(s):  
Mária Benkő ◽  
Á. Dán ◽  
et al. ◽  
R. Izadpanah
Keyword(s):  
Dna Sequence ◽  
Short Communication ◽  
Haemophilus Somnus

scholarly journals A DNA Sequence Based Polymer Model for Chromatin Folding

2021 ◽  
Vol 22 (3) ◽  
pp. 1328
Author(s):  
Rui Zhou ◽  
Yi Qin Gao
Keyword(s):  
Dna Sequence ◽  
Cpg Island ◽  
Coarse Grained ◽  
Chromosome Territories ◽  
Base Pairs ◽  
Single Chromosome ◽  
Power Law Decay ◽  
Multiple Length Scales ◽  
Spatial Domains ◽  
Chromatin Folding

The recent development of sequencing technology and imaging methods has provided an unprecedented understanding of the inter-phase chromatin folding in mammalian nuclei. It was found that chromatin folds into topological-associated domains (TADs) of hundreds of kilo base pairs (kbps), and is further divided into spatially segregated compartments (A and B). The compartment B tends to be located near to the periphery or the nuclear center and interacts with other domains of compartments B, while compartment A tends to be located between compartment B and interacts inside the domains. These spatial domains are found to highly correlate with the mosaic CpG island (CGI) density. High CGI density corresponds to compartments A and small TADs, and vice versa. The variation of contact probability as a function of sequential distance roughly follows a power-law decay. Different chromosomes tend to segregate to occupy different chromosome territories. A model that can integrate these properties at multiple length scales and match many aspects is highly desired. Here, we report a DNA-sequence based coarse-grained block copolymer model that considers different interactions between blocks of different CGI density, interactions of TAD formation, as well as interactions between chromatin and the nuclear envelope. This model captures the various single-chromosome properties and partially reproduces the formation of chromosome territories.

DNA sequence analysis of spontaneous mutations in the SUP4-o gene of Saccharomyces cerevisiae

1988 ◽  
Vol 8 (2) ◽  
pp. 978-981
Author(s):  
C N Giroux ◽  
J R Mis ◽  
M K Pierce ◽  
S E Kohalmi ◽  
B A Kunz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Sequence Analysis ◽  
Transposable Elements ◽  
Dna Sequencing ◽  
Dna Sequence ◽  
Base Pair ◽  
Dna Sequence Analysis ◽  
Spontaneous Mutations ◽  
Yeast Saccharomyces Cerevisiae ◽  
Spontaneous Mutagenesis

A collection of 196 spontaneous mutations in the SUP4-o gene of the yeast Saccharomyces cerevisiae was analyzed by DNA sequencing. The classes of mutation identified included all possible types of base-pair substitution, deletions of various lengths, complex alterations involving multiple changes, and insertions of transposable elements. Our findings demonstrate that at least several different mechanisms are responsible for spontaneous mutagenesis in S. cerevisiae.

Human c-fms proto-oncogene: comparative analysis with an abnormal allele

1985 ◽  
Vol 5 (2) ◽  
pp. 422-426
Author(s):  
J S Verbeek ◽  
A J Roebroek ◽  
A M van den Ouweland ◽  
H P Bloemers ◽  
W J Van de Ven
Keyword(s):  
Comparative Analysis ◽  
Dna Sequencing ◽  
Sequencing Analysis ◽  
Base Pairs ◽  
Small Deletion ◽  
Viral Oncogene ◽  
Close Proximity ◽  
Genetic Sequences ◽  
Dna Sequencing Analysis

The organization of the human c-fms proto-oncogene has been determined and compared with an abnormal allele. The human v-fms homologous genetic sequences are dispersed discontinuously and colinearly with the viral oncogene over a DNA region of ca. 32 kilobase pairs. The abnormal c-fms locus contains a small deletion in its 3' portion. DNA sequencing analysis indicated that it was 426 base pairs in size and located in close proximity to a putative c-fms exon.

scholarly journals Molecular confirmation of ovine herpesvirus 2-induced malignant catarrhal fever lesions in cattle from Rio Grande do Norte, Brazil

2012 ◽  
Vol 32 (12) ◽  
pp. 1213-1218 ◽  
Author(s):  
Selwyn A. Headley ◽  
Isadora K.F. Sousa ◽  
Antonio H.H. Minervino ◽  
Isabella O. Barros ◽  
Raimundo A. Barrêto Júnior ◽  
...  
Keyword(s):  
Lymph Node ◽  
Mesenteric Lymph Node ◽  
Protein Gene ◽  
Rio Grande ◽  
Corneal Opacity ◽  
Tegument Protein ◽  
Nasal Discharge ◽  
Malignant Catarrhal Fever ◽  
Base Pairs ◽  
Mesenteric Lymph

Molecular findings that confirmed the participation of ovine herpesvirus 2 (OVH-2) in the lesions that were consistent with those observed in malignant catarrhal fever of cattle are described. Three mixed-breed cattle from Rio Grande do Norte state demonstrated clinical manifestations that included mucopurulent nasal discharge, corneal opacity and motor incoordination. Routine necropsy examination demonstrated ulcerations and hemorrhage of the oral cavity, corneal opacity, and lymph node enlargement. Significant histopathological findings included widespread necrotizing vasculitis, non-suppurative meningoencephalitis, lymphocytic interstitial nephritis and hepatitis, and thrombosis. PCR assay performed on DNA extracted from kidney and mesenteric lymph node of one animal amplified a product of 423 base pairs corresponding to a target sequence within the ovine herpesvirus 2 (OVH-2) tegument protein gene. Direct sequencing of the PCR products, from extracted DNA of the kidney and mesenteric lymph node of one cow, amplified the partial nucleotide sequences (423 base pairs) of OVH-2 tegument protein gene. Blast analysis confirmed that these sequences have 98-100% identity with similar OVH-2 sequences deposited in GenBank. Phylogenetic analyses, based on the deduced amino acid sequences, demonstrated that the strain of OVH-2 circulating in ruminants from the Brazilian states of Rio Grande do Norte and Minas Gerais are similar to that identified in other geographical locations. These findings confirmed the active participation of OVH-2 in the classical manifestations of sheep associated malignant catarrhal fever.

scholarly journals Supercoiling DNA locates mismatches

2017 ◽  
Author(s):  
Andrew Dittmore ◽  
Sumitabha Brahmachari ◽  
Yasuhara Takagi ◽  
John F. Marko ◽  
Keir C. Neuman
Keyword(s):  
Dna Sequence ◽  
Base Pair ◽  
Dna Supercoiling ◽  
Magnetic Tweezers ◽  
Relative Probability ◽  
Base Pairs ◽  
Damage Sensing ◽  
Mismatched Base Pair ◽  
Monovalent Salt

We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3.5 pN force and show that, under these conditions, a single plectoneme forms and is stably pinned at the defect. We use these measurements to estimate the energy and degree of end-loop kinking at defects. From this, we calculate the relative probability of plectoneme pinning at the mismatch under physiologically relevant conditions. Based on this estimate, we propose that DNA supercoiling could contribute to mismatch and damage sensing in vivo.

DNA Sequence Analysis of Spontaneous Mutagenesis in Saccharomyces cerevisiae

Genetics ◽  
1998 ◽  
Vol 148 (4) ◽  
pp. 1491-1505 ◽  
Author(s):  
Bernard A Kunz ◽  
Karthikeyan Ramachandran ◽  
Edward J Vonarx
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Sequence Analysis ◽  
Dna Sequencing ◽  
Dna Sequence ◽  
Budding Yeast ◽  
Spontaneous Mutation ◽  
Dna Sequence Analysis ◽  
Mutation Rates ◽  
Yeast Saccharomyces Cerevisiae ◽  
Spontaneous Mutagenesis

AbstractTo help elucidate the mechanisms involved in spontaneous mutagenesis, DNA sequencing has been applied to characterize the types of mutation whose rates are increased or decreased in mutator or antimutator strains, respectively. Increased spontaneous mutation rates point to malfunctions in genes that normally act to reduce spontaneous mutation, whereas decreased rates are associated with defects in genes whose products are necessary for spontaneous mutagenesis. In this article, we survey and discuss the mutational specificities conferred by mutator and antimutator genes in the budding yeast Saccharomyces cerevisiae. The implications of selected aspects of the data are considered with respect to the mechanisms of spontaneous mutagenesis.

Octamer and SPH motifs in the U1 enhancer cooperate to activate U1 RNA gene expression

1990 ◽  
Vol 10 (1) ◽  
pp. 341-352
Author(s):  
K A Roebuck ◽  
D P Szeto ◽  
K P Green ◽  
Q N Fan ◽  
W E Stumph
Keyword(s):  
Dna Sequence ◽  
Functional Activity ◽  
Stable Complex ◽  
Small Nuclear Rna ◽  
Base Pairs ◽  
Rna Transcription ◽  
Octamer Motif ◽  
Chicken Tissue ◽  
Nuclear Rna ◽  
Gc Box

The transcriptional enhancer of a chicken U1 small nuclear RNA gene has been shown to extend over approximately 50 base pairs of DNA sequence located 180 to 230 base pairs upstream of the U1 transcription initiation site. It is composed of multiple functional motifs, including a GC box, an octamer motif, and a novel SPH motif. The contributions of these three distinct sequence motifs to enhancer function were studied with an oocyte expression assay. Under noncompetitive conditions in oocytes, the SPH motif is capable of stimulating U1 RNA transcription in the absence of the other functional motifs, whereas the octamer motif by itself lacks this ability. However, to form a transcription complex that is stable to challenge by a second competing small nuclear RNA transcription unit, both the octamer and SPH motifs are required. The GC box, although required for full enhancer activity, is not essential for stable complex formation in oocytes. Site-directed mutagenesis was used to study the DNA sequence requirements of the SPH motif. Functional activity of the SPH motif is spread throughout a 24-base-pair region 3' of the octamer but is particularly dependent upon sequences near an SphI restriction site located at the center of the SPH motif. Using embryonic chicken tissue as a source material, we identified and partially purified a factor, termed SBF, that binds sequence specifically to the SPH motif of the U1 enhancer. The ability of this factor to recognize and bind to mutant enhancer DNA fragments in vitro correlates with the functional activity of the corresponding enhancer sequences in vivo.

A new species of big-headed, fanged dicroglossine frog (Genus Limnonectes) from Thailand

Zootaxa ◽  
2008 ◽  
Vol 1807 (1) ◽  
pp. 26 ◽  
Author(s):  
DAVID S. McLEOD
Keyword(s):  
New Species ◽  
Dna Sequence ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Type Material ◽  
Base Pairs ◽  
Dna Sequence Data ◽  
16S Gene ◽  
A New Species

A new species of the dicroglossine genus Limnonectes from eastern Thailand and its tadpole are described. Analysis of DNA sequence data from 2518 base-pairs of the mitochondrial 12S and 16S gene regions places the species within the complex of frogs currently referred to as Limnonectes kuhlii and demonstrates it to be a separate lineage (>18% sequence divergence from type-material of L. kuhlii from Java). The new species differs from L. kuhlii by having nuptial pads, a greater snout–vent length, and different relative finger lengths than specimens from Java. It has more extensive toe webbing, a different arrangement of nuptial pads, and a greater snout–vent length than Limnonectes laticeps. The new species, which lacks vocal slits, also can be distinguished from the morphologically similar Limnonectes namiyei from Japan, which possesses vocal slits.

Sign in / Sign up

Export Citation Format

Share Document