DNA REASSOCIATION KINETICS OF FOUR CONIFERS

1980 ◽  
Vol 22 (1) ◽  
pp. 69-79 ◽  
Author(s):  
Adrian V. Rake ◽  
Jerome P. Miksche ◽  
Richard B. Hall ◽  
Kenneth M. Hansen
Keyword(s):  
Genome Size ◽  
Picea Glauca ◽  
Pinus Banksiana ◽  
Pinus Resinosa ◽  
Single Copy ◽  
Rrna Gene ◽  
Pinus Lambertiana ◽  
A Genome ◽  
Copy Dna ◽  
Kinetics Of

The DNA genome size of four conifers was determined cytophotometrically and the diploid amounts of DNA per cell of Picea glauca (Moench)Voss, Pinus banksiana Lamb., Pinus lambertiana Dougl., and Pinus resinosa Ait. were 19.3, 29.8, 87.7 and 43.1 pg., respectively. These DNA values yield rRNA gene numbers considerably lower than previously published (Hotta and Miksche, 1974). The DNA was further characterized by studying the kinetics of reassociation. The results indicated that in all four conifers there are four repeated nucleotide sequence fractions and one unique fraction. The genome size as determined by reassociation of the single copy DNA approximated the genome size determined by cytophotometry for Picea glauca and Pinus banksiana. Pinus lambertiana and Pinus resinosa appeared to have a genome size, as determined by cytophotometry, larger than the genome sizes determined by reassociation, indicating possible ploidy of their respective genomes.

DNA sequence organization in the starfish Dermasterias imbricata

1980 ◽  
Vol 58 (4) ◽  
pp. 352-360 ◽  
Author(s):  
Michael J. Smith ◽  
A. Lui ◽  
K. K. Gibson ◽  
J. K. Etzkorn
Keyword(s):  
Genomic Dna ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Sequence Organization ◽  
A Genome ◽  
Short Period ◽  
Nuclease Digestion ◽  
Kinetics Of

The sequence arrangement in the genomic DNA of the starfish Dermasterias imbricata has been examined. Analyses of kinetics of reassociation in solution at DNA lengths of 400, 3100, and 6200 base pairs (bp) demonstrate the interspersion of repetitive and unique DNA. At a fragment length of 400 bp, 45% of the DNA reacts at a rate appropriate for single-copy sequences in a genome of this size (0.54 pg). Interspersion of repetitive sequences is also demonstrated by the reduced hyperchromicity of 3100- or 6200-bp fragments reacted to Cot 10, where only repetitive sequences have formed duplex. S1 nuclease digestion of 3100-bp fragments reassociated to Cot 10 shows that both short (~ 230 bp) and long (≥ 2600 bp) repetitive sequences are present in this DNA. These data demonstrate a short period interspersion pattern in Dermasterias.

scholarly journals Aquirufa ecclesiirivi sp. nov. and Aquirufa beregesia sp. nov., isolated from a small creek and classification of Allopseudarcicella aquatilis as a later heterotypic synonym of Aquirufa nivalisilvae

2020 ◽  
Vol 70 (8) ◽  
pp. 4602-4609 ◽  
Author(s):  
Alexandra Pitt ◽  
Ulrike Koll ◽  
Johanna Schmidt ◽  
Martin W. Hahn
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Phylogenetic Reconstruction ◽  
Single Copy ◽  
Amino Acid Sequences ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
A Genome

Two bacterial strains, 50A-KIRBAT and 50C-KIRBAT, were isolated from the same freshwater creek located near Salzburg, Austria. They showed 16S rRNA gene sequence similarities to Aquirufa nivalisilvae of 100 and 99.9 %, respectively. A genome-based phylogenetic reconstruction with amino acid sequences of 119 single-copy genes suggested that the new strains represent two new species of the genus Aquirufa . Pairwise calculated whole-genome average nucleotide identity (gANI) values ranging from 85.4 to 87.5 % confirmed this conclusion. Phenotypic, chemotaxonomic and genomic traits were investigated. Like strains of other Aquirufa species, 50A-KIRBAT and 50C-KIRBAT grew aerobically and chemoorganotrophically, were rod-shaped, red-pigmented and motile, most likely by gliding. They could be distinguished by slight differences in the chemotaxonomic features. We propose to establish for strain 50A-KIRBAT (=CIP 111735T=LMG 31080T) as type strain the name Aquirufa ecclesiirivi and for strain 50C-KIRBAT (=CIP 111736T=LMG 31501T) as type strain the name Aquirufa beregesia. Furthermore, the relationship between the type strains of Aquirufa nivalisilvae (59G-WUEMPELT) and Allopseudarcicella aquatilis (HME7025T) was investigated. Results of polyphasic analyses, especially a gANI value of 97.6 %, as well as the genome-based phylogenetic reconstruction, suggested that Allopseudarcicella aquatilis is a heterotypic synonym of Aquirufa nivalisilvae . According to rule 24b of the International Code of Nomenclature of Prokaryotes we propose to classify strain HME7025 as Aquirufa nivalisilvae and provide an emended description for the latter.

A procedure for the purification of DNA from tobacco cell cultures and isolation of tobacco single-copy DNA

1978 ◽  
Vol 56 (12) ◽  
pp. 1453-1457 ◽  
Author(s):  
R. D. Locy ◽  
Ross H. Hall
Keyword(s):  
Melting Temperature ◽  
Cell Cultures ◽  
Buoyant Density ◽  
Single Copy ◽  
Tobacco Callus ◽  
Tobacco Cell ◽  
Reassociation Kinetics ◽  
Copy Dna ◽  
Kinetics Of ◽  
Single Copy Dna

A procedure is presented for the purification of DNA from tobacco callus cells. The procedure can be scaled up for the preparation in large quantity of DNA free of RNA, protein, and polysaccharide. The DNA prepared by this procedure has the same melting temperature and buoyant density as tobacco DNA prepared by previously published procedures and is of sufficient purity to be used for analysis of the reassociation kinetics of tobacco callus DNA. The DNA has been used as a source for the isolation of tobacco single-copy DNA.

scholarly journals The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa

2021 ◽  
Vol 9 (8) ◽  
pp. 1570
Author(s):  
Chien-Hsun Huang ◽  
Chih-Chieh Chen ◽  
Yu-Chun Lin ◽  
Chia-Hsuan Chen ◽  
Ai-Yun Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Target Genes ◽  
Marker Genes ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Discrimination Power ◽  
Sequence Identity ◽  
Genome Wide ◽  
A Genome

The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.

scholarly journals Ecofriendly Synthesis of Silver Nanoparticles by Terrabacter humi sp. nov. and Their Antibacterial Application against Antibiotic-Resistant Pathogens

2020 ◽  
Vol 21 (24) ◽  
pp. 9746
Author(s):  
Shahina Akter ◽  
Sun-Young Lee ◽  
Muhammad Zubair Siddiqi ◽  
Sri Renukadevi Balusamy ◽  
Md. Ashrafudoulla ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Spherical Shape ◽  
Optimal Growth ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Drug Resistant ◽  
Protein Coding ◽  
A Genome ◽  
The Fourier Transform

It is essential to develop and discover alternative eco-friendly antibacterial agents due to the emergence of multi-drug-resistant microorganisms. In this study, we isolated and characterized a novel bacterium named Terrabacter humi MAHUQ-38T, utilized for the eco-friendly synthesis of silver nanoparticles (AgNPs) and the synthesized AgNPs were used to control multi-drug-resistant microorganisms. The novel strain was Gram stain positive, strictly aerobic, milky white colored, rod shaped and non-motile. The optimal growth temperature, pH and NaCl concentration were 30 °C, 6.5 and 0%, respectively. Based on 16S rRNA gene sequence, strain MAHUQ-38T belongs to the genus Terrabacter and is most closely related to several Terrabacter type strains (98.2%–98.8%). Terrabacter humi MAHUQ-38T had a genome of 5,156,829 bp long (19 contigs) with 4555 protein-coding genes, 48 tRNA and 5 rRNA genes. The culture supernatant of strain MAHUQ-38T was used for the eco-friendly and facile synthesis of AgNPs. The transmission electron microscopy (TEM) image showed the spherical shape of AgNPs with a size of 6 to 24 nm, and the Fourier transform infrared (FTIR) analysis revealed the functional groups responsible for the synthesis of AgNPs. The synthesized AgNPs exhibited strong anti-bacterial activity against multi-drug-resistant pathogens, Escherichia coli and Pseudomonas aeruginosa. Minimal inhibitory/bactericidal concentrations against E. coli and P. aeruginosa were 6.25/50 and 12.5/50 μg/mL, respectively. The AgNPs altered the cell morphology and damaged the cell membrane of pathogens. This study encourages the use of Terrabacter humi for the ecofriendly synthesis of AgNPs to control multi-drug-resistant microorganisms.

Human XX males with Y single-copy DNA fragments

Nature ◽  
1984 ◽  
Vol 307 (5947) ◽  
pp. 172-173 ◽  
Author(s):  
Georges Guellaen ◽  
Myriam Casanova ◽  
Colin Bishop ◽  
Danielle Geldwerth ◽  
Gabriel Andre ◽  
...  
Keyword(s):  
Single Copy ◽  
Dna Fragments ◽  
Xx Males ◽  
Copy Dna ◽  
Single Copy Dna

scholarly journals Physical map of the Saccharomyces cerevisiae genome at 110-kilobase resolution.

Genetics ◽  
1991 ◽  
Vol 127 (4) ◽  
pp. 681-698 ◽  
Author(s):  
A J Link ◽  
M V Olson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Hybridization ◽  
Physical Map ◽  
Single Copy ◽  
Restriction Endonucleases ◽  
Yeast Genome ◽  
Hybridization Probes ◽  
Copy Dna ◽  
Single Copy Dna

Abstract A physical map of the Saccharomyces cerevisiae genome is presented. It was derived by mapping the sites for two restriction endonucleases, SfiI and NotI, each of which recognizes an 8-bp sequence. DNA-DNA hybridization probes for genetically mapped genes and probes that span particular SfiI and NotI sites were used to construct a map that contains 131 physical landmarks--32 chromosome ends, 61 SfiI sites and 38 NotI sites. These landmarks are distributed throughout the non-rDNA component of the yeast genome, which comprises 12.5 Mbp of DNA. The physical map suggests that those genes that can be detected and mapped by standard genetic methods are distributed rather uniformly over the full physical extent of the yeast genome. The map has immediate applications to the mapping of genes for which single-copy DNA-DNA hybridization probes are available.

scholarly journals DNA Genome Size Affects the Stability of the Adenovirus Virion

2008 ◽  
Vol 83 (4) ◽  
pp. 2025-2028 ◽  
Author(s):  
Adam C. Smith ◽  
Kathy L. Poulin ◽  
Robin J. Parks
Keyword(s):  
Genome Size ◽  
Critical Role ◽  
Heat Stability ◽  
Helper Virus ◽  
Heat Inactivation ◽  
Similar Relationship ◽  
Viral Dna ◽  
A Genome ◽  
The Stability ◽  
Replication Defective Adenovirus

ABSTRACT Replication-defective adenovirus (Ad) vectors can vary considerably in genome length, but whether this affects virion stability has not been investigated. Helper-dependent Ad vectors with a genome size of ∼30 kb were 100-fold more sensitive to heat inactivation than their parental helper virus (>36 kb), and increasing the genome size of the vector significantly improved heat stability. A similar relationship between genome size and stability existed for Ad with early region 1 deleted. Loss of infectivity was due to release of vertex proteins, followed by disintegration of the capsid. Thus, not only does the viral DNA encode all of the heritable information essential for virus replication, it also plays a critical role in maintaining capsid strength and integrity.

scholarly journals Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2080-2091 ◽  
Author(s):  
Anne-Laure Michon ◽  
Fabien Aujoulat ◽  
Laurent Roudière ◽  
Olivier Soulier ◽  
Isabelle Zorgniotti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Diversity ◽  
Natural Populations ◽  
Variable Region ◽  
Housekeeping Gene ◽  
Single Copy ◽  
Population Based ◽  
Rrna Gene ◽  
Gene Copies

As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter- and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel electrophoresis (TTGE). 16S rRNA gene diversity was high in the studied population, as 45 different banding patterns were observed. Intragenomic heterogeneity was demonstrated for 110 (74 %) isolates and 8 (61.5 %) type or reference strains displaying two or three different gene copies. Polymorphic nucleotide positions accounted for 0.5–2.5 % of the sequence and were scattered in helices H16 and H17 of the rRNA molecule. Some of them changed the secondary structure of H17. Phylotaxonomic structure of the population based on the single-copy housekeeping gene rpoB was compared with TTGE patterns. The intragenomic V3 heterogeneity, as well as recombination events between strains or isolates of different rpoB clades, impaired the 16S rRNA-based identification for some Veillonella species. Such approaches should be conducted in other bacterial populations to optimize the interpretation of 16S rRNA gene sequences in taxonomy and/or diversity studies.

A mammalian origin of bidirectional DNA replication within the Chinese hamster RPS14 locus

1994 ◽  
Vol 14 (9) ◽  
pp. 5628-5635
Author(s):  
E S Tasheva ◽  
D J Roufa
Keyword(s):  
Dna Replication ◽  
Chinese Hamster ◽  
Housekeeping Gene ◽  
Single Copy ◽  
The Other ◽  
Replication Origins ◽  
Chromosomal Replication ◽  
Dna Binding Sites ◽  
Sequence Encoding ◽  
Copy Dna

Two complementary experimental approaches have been used to identify a chromosomal origin of bidirectional DNA replication within or immediately downstream of the Chinese hamster ribosomal protein S14 gene (RPS14). The replication origin, designated oriS14, maps within a 1.6- to 2.0-kbp region of RPS14 that includes the gene's third and fourth introns, exons IV plus V, and approximately 500 bp of proximal downstream flanking DNA. The nucleic acid sequence encoding oriS14 closely resembles the other mammalian chromosomal replication origins whose primary structures are known. It contains DNA binding sites for a large number of transcription factors, replication proteins, and mammalian oncogenes as well as several dinucleotide repeat motifs, an AT-rich region, and a sequence that is likely to bend the DNA. In contrast to the other well-characterized mammalian replication origins, which are autosomal and therefore carried as two copies per somatic cell, oriS14 is encoded by single-copy DNA within a hemizygous segment of chromosome 2q in CHO-K1 cells. Also, other known mammalian replication origins are situated in nontranscribed, intergenic DNA, whereas the DNA sequence encoding oriS14 substantially overlaps the transcribed portion of a constitutively expressed housekeeping gene.

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