scholarly journals Circular Double-Stranded Forms of TT Virus DNA in the Liver

2000 ◽  
Vol 74 (11) ◽  
pp. 5161-5167 ◽  
Author(s):  
Hiroaki Okamoto ◽  
Masato Ukita ◽  
Tsutomu Nishizawa ◽  
Junichi Kishimoto ◽  
Yuji Hoshi ◽  
...  
Keyword(s):  
Human Beings ◽  
Specific Primer ◽  
Dna Virus ◽  
S1 Nuclease ◽  
Tt Virus ◽  
Double Stranded Dna ◽  
Replicative Intermediates ◽  
Paired Serum ◽  
Genomic Length ◽  
Liver Tissues

ABSTRACT TT virus (TTV) is an unenveloped, circular, and single-stranded DNA virus commonly infecting human beings worldwide. TTV DNAs in paired serum and liver tissues from three viremic individuals were separated by gel electrophoresis and characterized biophysically. TTV DNAs in sera migrated in sizes ranging from 2.0 to 2.5 kb. TTV DNAs in liver tissues, however, migrated at 2.0 to 2.5 kb as well as at 3.5 to 6.1 kb. Both faster- and slower-migrating forms of TTV DNAs in the liver were found to be circular and of the full genomic length of 3.8 kb. TTV DNAs migrating at 2.0 to 2.5 kb, from either serum or liver tissues, were sensitive to S1 nuclease but resistant to restriction endonucleases, and therefore, they were single-stranded. By contrast, TTV DNAs in liver tissues that migrated at 3.5 to 6.1 kb were resistant to S1 nuclease. They migrated at 3.7 to 4.0 kb after digestion with EcoRI, which suggests that they represent circular, double-stranded replicative intermediates of TTV. When TTV DNAs were subjected to strand-specific primer extension and then amplified by PCR with internal primers, those in serum were found to be minus-stranded DNAs while those in liver tissues were found to be a mixture of plus- and minus-stranded DNAs. These results suggest that TTV replicates in the liver via a circular double-stranded DNA.

scholarly journals Hierarchical dinucleotide distribution in genome along evolution and its effect on chromatin packing

2021 ◽  
Vol 4 (8) ◽  
pp. e202101028
Author(s):  
Zhicheng Cai ◽  
Yueying He ◽  
Sirui Liu ◽  
Yue Xue ◽  
Hui Quan ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Chromatin Structure ◽  
Distribution Patterns ◽  
Length Scales ◽  
Multi Scale ◽  
Topologically Associating Domain ◽  
Domain Boundaries ◽  
Chromatin Packing ◽  
The Difference ◽  
Genomic Length

Dinucleotide densities and their distribution patterns vary significantly among species. Previous studies revealed that CpG is susceptible to methylation, enriched at topologically associating domain boundaries and its distribution along the genome correlates with chromatin compartmentalization. However, the multi-scale organizations of CpG in the linear genome, their role in chromatin organization, and how they change along the evolution are only partially understood. By comparing the CpG distribution at different genomic length scales, we quantify the difference between the CpG distributions of different species and evaluate how the hierarchical uneven CpG distribution appears in evolution. The clustering of species based on the CpG distribution is consistent with the phylogenetic tree. Interestingly, we found the CpG distribution and chromatin structure to be correlated in many different length scales, especially for mammals and avians, consistent with the mosaic CpG distribution in the genomes of these species.

scholarly journals Genomic Analysis of Closely Related Astroviruses

2008 ◽  
Vol 82 (10) ◽  
pp. 5099-5103 ◽  
Author(s):  
Errol Strain ◽  
Laura A. Kelley ◽  
Stacey Schultz-Cherry ◽  
Spencer V. Muse ◽  
Matthew D. Koci
Keyword(s):  
Positive Selection ◽  
Genomic Analysis ◽  
Purifying Selection ◽  
Capsid Gene ◽  
Data Set ◽  
Site Specific ◽  
Factors Associated ◽  
Length Data ◽  
Genomic Length

ABSTRACT To understand astrovirus biology, it is essential to understand factors associated with its evolution. The current study reports the genomic sequences of nine novel turkey astrovirus (TAstV) type 2-like clinical isolates. This represents, to our knowledge, the largest genomic-length data set available for any one astrovirus type. The comparison of these TAstV sequences suggests that the TAstV species contains multiple subtypes and that recombination events have occurred across the astrovirus genome. In addition, the analysis of the capsid gene demonstrated evidence for both site-specific positive selection and purifying selection.

Electro-hydrodynamic concentration of genomic length DNA

Soft Matter ◽  
2016 ◽  
Vol 12 (33) ◽  
pp. 6975-6984 ◽  
Author(s):  
Mert Arca ◽  
Anthony J. C. Ladd ◽  
Jason E. Butler
Keyword(s):  
Genomic Length

scholarly journals HBV mutations in untreated HIV-HBV co-infection using genomic length sequencing

Virology ◽  
2010 ◽  
Vol 405 (2) ◽  
pp. 539-547 ◽  
Author(s):  
Jennifer Audsley ◽  
Margaret Littlejohn ◽  
Lilly Yuen ◽  
Joe Sasadeusz ◽  
Anna Ayres ◽  
...  
Keyword(s):  
Genomic Length

scholarly journals The dynamics of genomic-length DNA molecules in 100-nm channels

2004 ◽  
Vol 101 (30) ◽  
pp. 10979-10983 ◽  
Author(s):  
J. O. Tegenfeldt ◽  
C. Prinz ◽  
H. Cao ◽  
S. Chou ◽  
W. W. Reisner ◽  
...  
Keyword(s):  
Dna Molecules ◽  
Genomic Length

Biosystematic study of the Egyptian Datura stramonium (Solanaceae)

Phytotaxa ◽  
2019 ◽  
Vol 408 (3) ◽  
pp. 178-194
Author(s):  
RANIA A. HASSAN ◽  
WAFAA M. AMER
Keyword(s):  
Datura Stramonium ◽  
Distinct Species ◽  
Asymmetry Index ◽  
Pollen Characters ◽  
The World ◽  
Cytogenetic Studies ◽  
Morphological Differences ◽  
Intrachromosomal Asymmetry ◽  
Stem Colour ◽  
Genomic Length

Datura stramonium (Solanaceae) is an annual weed found in most temperate and subtropical regions of the world. The taxonomic identity of this species is still under debate since Linnaeus first published the name. Early on, many varieties and forms were recognized. In Egypt, D. stramonium presents in two forms: the white-flowered ‘stramonium’ form and violet-flowered ‘tatula’ form. Some authors treated D. stramonium and D. tatula as two distinct species, while others included D. tatula within D. stramonium as either a variety or forma. The present study aimed to elucidate the taxonomic identity of both the white ‘stramonium’ and the violet ‘tatula’ forms based on morphological, palynological and cytogenetic studies extended to karyotyping. A taxonomic study of these forms was carried out using 75 morphological and pollen characters. Significant morphological differences were observed; the most important ones were flower and stem colour, in addition to flower and fruit dimensions. The anatomical examination of juvenile-fruit in acropetal transverse sections, revealed the gradual displacement of parietal placentation at the fruit base to axile at the fruit apex. Pollen of both forms showed no significant differences. Cytogenetic results revealed the presence of a diploid chromosome number (2n=2x=24) in both forms, with minor aneuploidy in the ‘tatula’ form. According to the karyotyping, notable differences were found between the two studied forms, including the centromeric index, total genomic length, and intrachromosomal asymmetry index. Morphological and cytogenetic data revealed that the two forms are different enough to be treated taxonomically as two distinct varieties, namely D. stramonium var. stramonium and D. stramonium var. tatula.

scholarly journals Fish and chips: the origin of human gene families is a predictor of the location of GWAS signals

2021 ◽  
Author(s):  
Sara Victoria Good ◽  
Ryan Gotesman ◽  
Ilya Kisselev ◽  
Andrew D. Paterson
Keyword(s):  
Human Gene ◽  
Gene Families ◽  
Selective Constraint ◽  
Variant Prioritization ◽  
Gene Level ◽  
And Function ◽  
Genomic Length ◽  
Human Complex ◽  
Gwas Catalog ◽  
Median Expression

Abstract GWAS have identified thousands of loci associated with human complex diseases and traits. How these loci are distributed through the genome has not been systematically evaluated. We hypothesised that the location of GWAS loci differ between ancestral linkage groups (ALGs) related to the paralogy and function of genes. We used data from the NHGRI-EBI GWAS catalog to determine whether the density of GWAS loci relative to HapMap variants in each ALG differed, and whether ALG’s were enriched for experimental factor ontological (EFO) terms assigned to the GWAS traits. In a gene-level analyses we explored the characteristics of genes linked to GWAS loci and those mapping to the ALG’s. We find that GWAS loci were enriched or deficient in 9 and 7 of the 17 ALG’s respectively, while there was no difference in the number of GWAS loci in regions of the human genome unassigned to an ALG. All but 2 ALG’s were significantly enriched or deficient for one or more EFO terms. Lastly, we find that genes assigned to an ALG are under higher levels of selective constraint, have longer coding sequences and higher median expression in the tissue of highest expression than genes not mapping to an ALG. On the other hand, genes associated with GWAS loci have longer genomic length and exhibit higher levels of selective constraint relative to non-GWAS genes.Collectively, this suggests that understanding the location and ancestral origins of GWAS signals may be informative for the development of tools for variant prioritization and interpretation.

scholarly journals Minimal-assumption inference from population-genomic data

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Daniel B Weissman ◽  
Oskar Hallatschek
Keyword(s):  
Evolutionary History ◽  
Simulated Data ◽  
Large Samples ◽  
Minimal Assumption ◽  
Population Genomic ◽  
Human Genomes ◽  
History Of ◽  
Or Gene ◽  
Linked Selection ◽  
Genomic Length

Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. We introduce a method, Minimal-Assumption Genomic Inference of Coalescence (MAGIC), that reconstructs key features of the evolutionary history, including the distribution of coalescence times, by integrating information across genomic length scales without using an explicit model of coalescence or recombination, allowing it to analyze arbitrarily large samples without phasing while making no assumptions about ancestral structure, linked selection, or gene conversion. Using simulated data, we show that the performance of MAGIC is comparable to that of PSMC’ even on single diploid samples generated with standard coalescent and recombination models. Applying MAGIC to a sample of human genomes reveals evidence of non-demographic factors driving coalescence.

scholarly journals Identification and genomic characterization of a novel human torque teno virus of 3.2 kb

2007 ◽  
Vol 88 (7) ◽  
pp. 1939-1944 ◽  
Author(s):  
Masashi Ninomiya ◽  
Tsutomu Nishizawa ◽  
Masaharu Takahashi ◽  
Felipe R. Lorenzo ◽  
Tooru Shimosegawa ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Torque Teno Virus ◽  
The Novel ◽  
Entire Genome ◽  
Human Sera ◽  
Genomic Characterization ◽  
Novel Virus ◽  
Entire Genomic Sequence ◽  
Genomic Length

In the process of searching for the recently described small anelloviruses 1 and 2 (SAVs) with the genomic DNA length of 2.2 or 2.6 kb in human sera, we isolated a novel virus with its genomic organization resembling those of torque teno virus (TTV) of 3.8–3.9 kb and torque teno mini virus (TTMV) of 2.8–2.9 kb. The entire genomic sequence of three isolates (MD1-032, MD1-073 and MD2-013), which comprised 3242–3253 bases and exhibited 76–99 % identities with the SAVs within the overlapping sequence, was determined. Although the MD1-032, MD1-073 and MD2-013 isolates differed by 10–28 % from each other over the entire genome, they segregated into the same cluster and were phylogenetically distinguishable from all reported TTVs and TTMVs. These results suggest that SAVs are deletion mutants of the novel virus with intermediate genomic length between those of TTV and TTMV and that the novel virus can be classified into a third group of the genus Anellovirus.

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