scholarly journals Circular Rep-Encoding Single-Stranded DNA Sequences in Milk from Water Buffaloes (Bubalus arnee f. bubalis)

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1088
Author(s):  
Marie-T. König ◽  
Robert Fux ◽  
Ellen Link ◽  
Gerd Sutter ◽  
Erwin Märtlbauer ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Western Europe ◽  
Tandem Repeats ◽  
Water Buffaloes ◽  
Isolation And Characterization ◽  
Circular Dnas ◽  
Dna Elements ◽  
Characteristic Features ◽  
High Degree ◽  
Asian Water

Isolation and characterization of circular replicase-encoding single-stranded (ss) DNA from animal, plant and environmental samples are rapidly evolving in virology. We detected 21 circular DNA elements, including one genomoviral sequence, in individual milk samples from domesticated Asian water buffaloes (Bubalus arnee f. bubalis). Most of the obtained genomes are related to Sphinx 1.76 and Sphinx 2.36 sequences and share a high degree of similarity to recently published circular DNAs—named BMMF (bovine meat and milk factors)—that have been isolated from commercial milk, as well as from bovine serum. Characteristic features such as rep genes, tandem repeats and inverted repeats were detected. These BMMF have recently been found to be present in taurine-type dairy cattle breeds descending from the aurochs (Bos primigenius). Importantly, the occurrence of BMMF has been linked to the higher incidence of colorectal and breast cancer in North America and Western Europe compared with Asia. This is the first report of circular ssDNA detected in milk from the domesticated form of the wild Asian water buffalo (B. arnee) belonging to the subfamily Bovinae. This novelty should be taken into account in view of the above-mentioned cancer hypothesis.

Highly Condensed Potato Pericentromeric Heterochromatin Contains rDNA-Related Tandem Repeats

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1435-1444 ◽  
Author(s):  
Robert M Stupar ◽  
Junqi Song ◽  
Ahmet L Tek ◽  
Zhukuan Cheng ◽  
Fenggao Dong ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Intergenic Spacer ◽  
Pericentromeric Heterochromatin ◽  
Dna Repeats ◽  
Solanum Bulbocastanum ◽  
Origin And Evolution ◽  
Potato Genome ◽  
Dna Elements

Abstract The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S•25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.

Cloning and characterization of the majority of repetitive DNA in cotton (Gossypium L.)

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1177-1188 ◽  
Author(s):  
Xinping Zhao ◽  
Rod A. Wing ◽  
Andrew H. Paterson
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Repetitive Sequences ◽  
Repetitive Dna Sequences ◽  
Tetraploid Cotton ◽  
Cotton Genome ◽  
Cotton Species ◽  
Dna Elements ◽  
Repetitive Dna Elements

Repetitive DNA elements representing 60–70% of the total repetitive DNA in tetraploid cotton (Gossypium barbadense L.) and comprising 30–36% of the tetraploid cotton genome were isolated from a genomic library of DNA digested with a mixture of four blunt-end cutting restriction enzymes. A total of 313 clones putatively containing nuclear repetitive sequences were classified into 103 families, based on cross hybridization and Southern blot analysis. The 103 families were characterized in terms of genome organization, methylation pattern, abundance, and DNA variation. As in many other eukaryotic genomes, interspersed repetitive elements are the most abundant class of repetitive DNA in the cotton genome. Paucity of tandem repeat families with high copy numbers (>104) may be a unique feature of the cotton genome as compared with other higher plant genomes. Interspersed repeats tend to be methylated, while tandem repeats seem to be largely unmethylated in the cotton genome. Minimal variation in repertoire and overall copy number of repetitive DNA elements among different tetraploid cotton species is consistent with the hypothesis of a relatively recent origin of tetraploid cottons.Key words: genome analysis, genome evolution, tandemly repetitive DNA sequences, interspersed repetitive DNA sequences, polyploid.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

Introduction

2017 ◽  
Author(s):  
Detlef Pollack ◽  
Gergely Rosta
Keyword(s):  
The Netherlands ◽  
Western Europe ◽  
West Germany ◽  
World Today ◽  
The World ◽  
Degree Of Stability ◽  
Important Exception ◽  
High Degree ◽  
Religious Landscape

In recantation of his earlier approach, Peter L. Berger now claims: ‘The world today, with some exceptions […], is as furiously religious as it ever was, and in some places more so than ever.’ The most important exception that Berger refers to is Western Europe. The introduction to Part II provides an overview of the religious landscape in Western Europe. The data show that the current religious situation in the countries of Western Europe is in fact subject to considerable variation. It would therefore be erroneous to describe Western Europe as secularized. At the same time, the data reveal that there have been clear secularization tendencies over the last few decades. To grasp the diversity of religious tendencies, Part II deals with three cases: West Germany with moderate downward tendencies, Italy with a considerably high degree of stability, and the Netherlands displaying disproportionately strong secularizing tendencies.

scholarly journals Small-mammal assemblages inhabiting Sphagnum peat bogs in various regions of Poland

2012 ◽  
Vol 49 (2) ◽  
pp. 115-133
Author(s):  
Mateusz Ciechanowski ◽  
Jan Cichocki ◽  
Agnieszka Ważna ◽  
Barbara Piłacińska
Keyword(s):  
Small Mammal ◽  
Western Europe ◽  
Habitat Degradation ◽  
Myodes Glareolus ◽  
Peat Bogs ◽  
Trophic Conditions ◽  
Characteristic Features ◽  
Mammal Assemblages ◽  
Sorex Minutus ◽  
Pygmy Shrew

Abstract We studied species composition of assemblages of small mammals (rodents and shrews) inhabiting Polish 25 ombrotrophic mires and quaking bogs in several regions in order to reveal characteristic features of their quantitative structure and compare them between regions, internal zones of the bog habitats, and different levels of anthropogenic degradation. We reviewed also all published results of small-mammal trapping in such habitats. Mammals were captured in pitfalls, snap traps and live traps on 12 bogs of the Pomerania region, 4 bogs of the Orawa-Nowy Targ Basin (Kotlina Orawsko-Nowotarska), 3 bogs in the Świętokrzyskie Mts, and 6 bogs in Wielkopolska and the Lubusz Land. Additionally, we included materials collected from Barber traps (pitfalls) used during studies of epigeic invertebrates on 4 bogs. In total, 598 individuals of 12 species were collected. The number of pitfall captures per 100 trapnights was very low (7.0-7.8), suggesting low population density. Shrews predominated among mammals captured in pitfalls, and the assemblage structure appeared to be similar to impoverished forest fauna, slightly enriched with ubiquitous species from meadows and agroecosystems, with a very small percentage of typical wetland species (Neomys fodiens, Neomys anomalus, Microtus oeconomus). Rodents (mostly Myodes glareolus) predominated only in samples obtained by live and snap traps. Pygmy shrew Sorex minutus was the most numerous species at most sites, sometimes being the only small mammal in that habitat, especially in well-preserved, treeless parts of bogs, dominated by Sphagnum peatmoss. The dominance and high constancy of S. minutus appear to be a characteristic feature of small-mammal assemblages inhabiting ombrotrophic mires, at least in some regions of Central and Western Europe. Enrichment of the fauna with other species might be related to either improved trophic conditions (by contact with mineralized ground waters) or habitat degradation (by peat mining, drainage, and subsequent secondary succession).

scholarly journals Structural differences and the presence of unsubstituted amino groups in heparan sulphates from different tissues and species

1997 ◽  
Vol 322 (2) ◽  
pp. 499-506 ◽  
Author(s):  
Toshihiko TOIDA ◽  
Hisao YOSHIDA ◽  
Hidenao TOYODA ◽  
Ichiro KOSHIISHI ◽  
Toshio IMANARI ◽  
...  
Keyword(s):  
Acid Content ◽  
Heparan Sulphate ◽  
Kidney Medulla ◽  
Isolation And Characterization ◽  
Iduronic Acid ◽  
Structural Differences ◽  
Liver And Kidney ◽  
High Degree ◽  
Different Tissues

This study presents a comparison of heparan sulphate chains isolated from various porcine and bovine tissues. 1H-NMR spectroscopy (500 MHz) was applied for structural and compositional studies on intact heparan sulphate chains. After enzymic digestion of heparan sulphate using heparin lyase I (EC 4.2.2.7) II and III (EC 4.2.2.8), the compositions of unsaturated disaccharides obtained were determined by analytical capillary electrophoresis. Correlations between the N-sulphated glucosamine residues and O-sulphation and between iduronic acid content and total sulphation were discovered using the data obtained by NMR and disaccharide analysis. Heparan sulphate chains could be classified into two groups based on the sulphation degree and the iduronic acid content. Heparan sulphate chains with a high degree of sulphation possessed also a significant number of iduronic acid residues and were isolated exclusively from porcine brain, liver and kidney medulla. The presence and amount of N-unsubstituted glucosamine residues (GlcNp) was established in all of the heparan sulphates examined. The structural context in which this residue occurs was demonstrated to be: high sulphation domain → 4)-β-d-GlcAp-(1 → 4)-α-d-GlcNp-(1 → 4)-β-d-GlcAp-(1 → low sulphation domain (where GlcNp is 2-amino-2-deoxyglucopyranose, and GlcAp is glucopyranosyluronic acid), based on the isolation and characterization of a novel, heparin lyase III-derived, GlcNp containing tetrasaccharide and hexasaccharide. The results presented suggest that structural differences may play a role in important biological events controlled by heparan sulphate in different tissues.

scholarly journals Isolation and characterization of adrenocortical progenitors involved in the adaptation to stress

2018 ◽  
Vol 115 (51) ◽  
pp. 12997-13002 ◽  
Author(s):  
Charlotte Steenblock ◽  
Maria F. Rubin de Celis ◽  
Luis F. Delgadillo Silva ◽  
Verena Pawolski ◽  
Ana Brennand ◽  
...  
Keyword(s):  
Lineage Tracing ◽  
Differentiated Cells ◽  
Isolation And Characterization ◽  
Proliferation And Differentiation ◽  
Response To Stress ◽  
Steroidogenic Cells ◽  
High Degree

The adrenal gland is a master regulator of the human body during response to stress. This organ shows constant replacement of senescent cells by newly differentiated cells. A high degree of plasticity is critical to sustain homeostasis under different physiological demands. This is achieved in part through proliferation and differentiation of adult adrenal progenitors. Here, we report the isolation and characterization of a Nestin+ population of adrenocortical progenitors located under the adrenal capsule and scattered throughout the cortex. These cells are interconnected with progenitors in the medulla. In vivo lineage tracing revealed that, under basal conditions, this population is noncommitted and slowly migrates centripetally. Under stress, this migration is greatly enhanced, and the cells differentiate into steroidogenic cells. Nestin+ cells cultured in vitro also show multipotency, as they differentiate into mineralocorticoid and glucocorticoid-producing cells, which can be further influenced by the exposure to Angiotensin II, adrenocorticotropic hormone, and the agonist of luteinizing hormone-releasing hormone, triptorelin. Taken together, Nestin+ cells in the adult adrenal cortex exhibit the features of adrenocortical progenitor cells. Our study provides evidence for a role of Nestin+ cells in organ homeostasis and emphasizes their role under stress. This cell population might be a potential source of cell replacement for the treatment of adrenal insufficiency.

Audiological Features and Mitochondrial DNA Sequence in a Large Family Carrying Mitochondrial A1555G Mutation without Use of Aminoglycoside

2005 ◽  
Vol 114 (2) ◽  
pp. 153-160 ◽  
Author(s):  
Tatsuo Matsunaga ◽  
Hiroshi Kumanomido ◽  
Yu-ichi Goto ◽  
Masae Shiroma ◽  
Shin-ichi Usami
Keyword(s):  
Hearing Loss ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Large Family ◽  
Outer Hair Cells ◽  
Japanese Family ◽  
A1555g Mutation ◽  
Genetic Mechanisms ◽  
High Degree ◽  
Sibling Group

To elucidate the pathophysiological and genetic mechanisms of hearing loss associated with the homoplasmic mitochondrial A1555G mutation in the absence of aminoglycoside exposure, we conducted audiological and genetic analyses on 67 maternally related members of a large Japanese family carrying this mutation. A consistent pattern was evident in the audiograms, with features of sensory presbycusis, cochlear origin at all levels of hearing loss, and a high degree of vulnerability of outer hair cells. That the degree of hearing loss was similar in affected subjects within the same sibling group but differed between sibling groups suggests the involvement of nuclear modifier genes. Total mitochondrial DNA sequences were completely identical among subjects with various levels of hearing loss, and lacked additional pathogenic mutations. For the diagnosis of sensorineural hearing loss, the mitochondrial A1555G mutation should be considered when these features are present even in the absence of aminoglycoside exposure.

Molecular and cytogenetic analysis of repetitive DNA in pea (Pisum sativum L.)

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 716-728 ◽  
Author(s):  
Pavel Neumann ◽  
Marcela Nouzová ◽  
Jirí Macas
Keyword(s):  
Pisum Sativum ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Genomic Library ◽  
Chromosome Morphology ◽  
Plant Genome ◽  
Genomic Repeats ◽  
Dispersed Repeats

A set of pea DNA sequences representing the most abundant genomic repeats was obtained by combining several approaches. Dispersed repeats were isolated by screening a short-insert genomic library using genomic DNA as a probe. Thirty-two clones ranging from 149 to 2961 bp in size and from 1000 to 39 000/1C in their copy number were sequenced and further characterized. Fourteen clones were identified as retrotransposon-like sequences, based on their homologies to known elements. Fluorescence in situ hybridization using clones of reverse transcriptase and integrase coding sequences as probes revealed that corresponding retroelements were scattered along all pea chromosomes. Two novel families of tandem repeats, named PisTR-A and PisTR-B, were isolated by screening a genomic DNA library with Cot-1 DNA and by employing genomic self-priming PCR, respectively. PisTR-A repeats are 211–212 bp long, their abundance is 2 × 104 copies/1C, and they are partially clustered in a secondary constriction of one chromosome pair with the rest of their copies dispersed on all chromosomes. PisTR-B sequences are of similar abundance (104 copies/1C) but differ from the "A" family in their monomer length (50 bp), high A/T content, and chromosomal localization in a limited number of discrete bands. These bands are located mainly in (sub)telomeric and pericentromeric regions, and their patterns, together with chromosome morphology, allow discrimination of all chromosome types within the pea karyotype. Whereas both tandem repeat families are mostly specific to the genus Pisum, many of the dispersed repeats were detected in other legume species, mainly those in the genus Vicia.Key words: repetitive DNA, plant genome, retroelements, satellite DNA, Pisum sativum.

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