Characterization of putative circular plasmids in sponge‐associated bacterial communities using a selective multiply‐primed rolling circle amplification

2020 ◽  
Vol 21 (1) ◽  
pp. 110-121
Author(s):  
Vanessa Oliveira ◽  
Ana R. M. Polónia ◽  
Daniel F. R. Cleary ◽  
Yusheng M. Huang ◽  
Nicole J. Voogd ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Rolling Circle Amplification ◽  
Rolling Circle

scholarly journals Characterization of Two Novel Polyomaviruses of Birds by Using Multiply Primed Rolling-Circle Amplification of Their Genomes

2006 ◽  
Vol 80 (7) ◽  
pp. 3523-3531 ◽  
Author(s):  
Reimar Johne ◽  
Walter Wittig ◽  
Daniel Fernández-de-Luco ◽  
Ursula Höfle ◽  
Hermann Müller
Keyword(s):  
Rolling Circle Amplification ◽  
Large Tumor ◽  
Rolling Circle ◽  
Reading Frame ◽  
Field Samples ◽  
Close Relationship ◽  
Avian Polyomavirus ◽  
Avian Group ◽  
Pyrrhula Pyrrhula

ABSTRACT Polyomaviruses are small nonenveloped particles with a circular double-stranded genome, approximately 5 kbp in size. The mammalian polyomaviruses mainly cause persistent subclinical infections in their natural nonimmunocompromised hosts. In contrast, the polyomaviruses of birds—avian polyomavirus (APV) and goose hemorrhagic polyomavirus (GHPV)—are the primary agents of acute and chronic disease with high mortality rates in young birds. Screening of field samples of diseased birds by consensus PCR revealed the presence of two novel polyomaviruses in the liver of an Eurasian bullfinch (Pyrrhula pyrrhula griseiventris) and in the spleen of a Eurasian jackdaw (Corvus monedula), tentatively designated as finch polyomavirus (FPyV) and crow polyomavirus (CPyV), respectively. The genomes of the viruses were amplified by using multiply primed rolling-circle amplification and cloned. Analysis of the FPyV and CPyV genome sequences revealed a close relationship to APV and GHPV, indicating the existence of a distinct avian group among the polyomaviruses. The main characteristics of this group are (i) involvement in fatal disease, (ii) the existence of an additional open reading frame in the 5′ region of the late mRNAs, and (iii) a different manner of DNA binding of the large tumor antigen compared to that of the mammalian polyomaviruses.

scholarly journals Circular genomes related to anelloviruses identified in human and animal samples by using a combined rolling-circle amplification/sequence-independent single primer amplification approach

2007 ◽  
Vol 88 (10) ◽  
pp. 2696-2701 ◽  
Author(s):  
Philippe Biagini ◽  
Rathviro Uch ◽  
Mourad Belhouchet ◽  
Houssam Attoui ◽  
Jean-François Cantaloube ◽  
...  
Keyword(s):  
Human Plasma ◽  
Genetic Divergence ◽  
Rolling Circle Amplification ◽  
Plasma Samples ◽  
Rolling Circle ◽  
Human Plasma Samples ◽  
Single Primer ◽  
Divergent Sequences

A combined rolling-circle amplification (RCA) and sequence-independent single primer amplification (SISPA) approach was applied to four samples of human plasma and one sample of saliva from a cat. This approach permitted the characterization of nine anelloviruses. Most of them were identified as highly divergent strains that were classified into species of the genus Anellovirus. The smallest anellovirus described so far in humans was characterized (2PoSMA, 2002 nt; ‘small anellovirus’ species). Two highly divergent sequences belonging to the species Torque Teno Mini Virus (LIL-y1, 2887 nt; LIL-y2, 2871 nt), which clustered into a new phylogenetic branch, were also identified in human plasma samples. Finally, two genomes that are separated by a genetic divergence of 46 % were characterized in the cat's saliva, one of these creating a distinct phylogenetic branch (PRA1, 2019 nt). These results highlight the potential of RCA–SISPA for detecting circular (or circularized) genomes.

scholarly journals Reconstruction and Characterization of Full-Length Begomovirus and Alphasatellite Genomes Infecting Pepper through Metagenomics

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 202 ◽  
Author(s):  
Verónica A. Bornancini ◽  
José M. Irazoqui ◽  
Ceferino R. Flores ◽  
Carlos G. Vaghi Medina ◽  
Ariel F. Amadio ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Full Length ◽  
Yellow Spot ◽  
Streak Virus ◽  
Rolling Circle ◽  
Viral Particles ◽  
Bipartite Genome ◽  
First Time ◽  
Leaf Virus

In northwestern Argentina (NWA), pepper crops are threatened by the emergence of begomoviruses due to the spread of its vector, Bemisia tabaci (Gennadius). The genus Begomovirus includes pathogens that can have a monopartite or bipartite genome and are occasionally associated with sub-viral particles called satellites. This study characterized the diversity of begomovirus and alphasatellite species infecting pepper in NWA using a metagenomic approach. Using RCA-NGS (rolling circle amplification-next generation sequencing), 19 full-length begomovirus genomes (DNA-A and DNA-B) and one alphasatellite were assembled. This ecogenomic approach revealed six begomoviruses in single infections: soybean blistering mosaic virus (SbBMV), tomato yellow spot virus (ToYSV), tomato yellow vein streak virus (ToYVSV), tomato dwarf leaf virus (ToDfLV), sida golden mosaic Brazil virus (SiGMBRV), and a new proposed species, named pepper blistering leaf virus (PepBLV). SbBMV was the most frequently detected species, followed by ToYSV. Moreover, a new alphasatellite associated with ToYSV, named tomato yellow spot alphasatellite 2 (ToYSA-2), was reported for the first time in Argentina. For the Americas, this was the first report of an alphasatellite found in a crop (pepper) and in a weed (Leonurus japonicus). We also detected intra-species and inter-species recombination.

scholarly journals Characterization of Binding of Magnetic Nanoparticles to Rolling Circle Amplification Products by Turn-On Magnetic Assay

Biosensors ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 109 ◽  
Author(s):  
Sobhan Sepehri ◽  
Björn Agnarsson ◽  
Teresa Zardán Gómez de la Torre ◽  
Justin F. Schneiderman ◽  
Jakob Blomgren ◽  
...  
Keyword(s):  
Magnetic Nanoparticles ◽  
Specific Binding ◽  
Ac Susceptibility ◽  
Rolling Circle Amplification ◽  
Rolling Circle ◽  
Low Concentrations ◽  
Assay Performance ◽  
Particle Ensemble ◽  
Kinetics Of

The specific binding of oligonucleotide-tagged 100 nm magnetic nanoparticles (MNPs) to rolling circle products (RCPs) is investigated using our newly developed differential homogenous magnetic assay (DHMA). The DHMA measures ac magnetic susceptibility from a test and a control samples simultaneously and eliminates magnetic background signal. Therefore, the DHMA can reveal details of binding kinetics of magnetic nanoparticles at very low concentrations of RCPs. From the analysis of the imaginary part of the DHMA signal, we find that smaller MNPs in the particle ensemble bind first to the RCPs. When the RCP concentration increases, we observe the formation of agglomerates, which leads to lower number of MNPs per RCP at higher concentrations of RCPs. The results thus indicate that a full frequency range of ac susceptibility observation is necessary to detect low concentrations of target RCPs and a long amplification time is not required as it does not significantly increase the number of MNPs per RCP. The findings are critical for understanding the underlying microscopic binding process for improving the assay performance. They furthermore suggest DHMA is a powerful technique for dynamically characterizing the binding interactions between MNPs and biomolecules in fluid volumes.

scholarly journals Genomic characterization of ten novel cutaneous human papillomaviruses from keratotic lesions of immunosuppressed patients

2011 ◽  
Vol 92 (7) ◽  
pp. 1585-1594 ◽  
Author(s):  
Anja Köhler ◽  
Marc Gottschling ◽  
Kizzie Manning ◽  
Mandy D. Lehmann ◽  
Eric Schulz ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Rolling Circle Amplification ◽  
Organ Transplant ◽  
Human Papillomaviruses ◽  
Rolling Circle ◽  
Non Melanoma Skin Cancer ◽  
Immunosuppressed Patients ◽  
Genomic Characterization ◽  
Hpv Types

Viral warts from immunosuppressed organ transplant recipients (OTR) persist over years and may progress into non-melanoma skin cancer. The types of human papillomaviruses (HPV) in such lesions are different from that seen in the general population. A subset of these lesions is not infected with the classical wart-associated HPV types. In order to gain a better understanding of the HPV types in those lesions, we isolated ten novel HPVs from persisting keratotic lesions of immunosuppressed OTRs by rolling circle amplification and subsequent long-template PCR. Additionally, we sequenced and characterized the whole genome of the ten novel HPV types. Phylogenetic analyses revealed that nine HPV types belonged to the genus Gammapapillomavirus (γ-PV) and one to the genus Betapapillomavirus. In a phylogenetic analysis using L1 fragments of human and non-human PV types, primate papillomaviruses and our novel HPV types nested within the genus γ-PV in a highly polyphyletic pattern. This study significantly broadens the knowledge concerning the diversity and evolution of the poorly known γ-PV types.

scholarly journals Assessment and optimization of rolling circle amplification protocols for the detection and characterization of badnaviruses

Virology ◽  
2019 ◽  
Vol 529 ◽  
pp. 73-80 ◽  
Author(s):  
Amit C. Sukal ◽  
Dawit B. Kidanemariam ◽  
James L. Dale ◽  
Robert M. Harding ◽  
Anthony P. James
Keyword(s):  
Rolling Circle Amplification ◽  
Rolling Circle

scholarly journals Characterization of a Novel Close-to-Root Papillomavirus from a Florida Manatee by Using Multiply Primed Rolling-Circle Amplification: Trichechus manatus latirostris Papillomavirus Type 1

2004 ◽  
Vol 78 (22) ◽  
pp. 12698-12702 ◽  
Author(s):  
Annabel Rector ◽  
Gregory D. Bossart ◽  
Shin-Je Ghim ◽  
John P. Sundberg ◽  
A. Bennett Jenson ◽  
...  
Keyword(s):  
Marine Mammals ◽  
Rolling Circle Amplification ◽  
Phylogenetic Position ◽  
Florida Manatee ◽  
Trichechus Manatus ◽  
Trichechus Manatus Latirostris ◽  
Rolling Circle ◽  
Amplification Protocol

ABSTRACT By using an isothermal multiply primed rolling-circle amplification protocol, the complete genomic DNA of a novel papillomavirus was amplified from a skin lesion biopsy of a Florida manatee (Trichechus manatus latirostris), one of the most endangered marine mammals in United States coastal waters. The nucleotide sequence, genome organization, and phylogenetic position of the Trichechus manatus latirostris papillomavirus type 1 (TmPV-1) were determined. TmPV-1 is the first virus isolated from the order of Sirenia. A phylogenetic analysis shows that TmPV-1 is only distantly related to other papillomavirus sequences, and it appears in our phylogenetic tree as a novel close-to-root papillomavirus genus.

scholarly journals Development of a Novel Rolling-Circle Amplification Technique to Detect Banana streak virus that also Discriminates Between Integrated and Episomal Virus Sequences

Plant Disease ◽  
2011 ◽  
Vol 95 (1) ◽  
pp. 57-62 ◽  
Author(s):  
A. P. James ◽  
R. J. Geijskes ◽  
J. L. Dale ◽  
R. M. Harding
Keyword(s):  
Rolling Circle Amplification ◽  
Cauliflower Mosaic Virus ◽  
Diagnostic Methods ◽  
Streak Virus ◽  
Banana Streak Virus ◽  
Rolling Circle ◽  
Sugarcane Bacilliform Virus ◽  
Amplification Technique ◽  
Banana Streak Ol Virus

Banana plants are hosts to a large number of Banana streak virus (BSV) species. However, diagnostic methods for BSV are inadequate because of the considerable genetic and serological diversity among BSV isolates and the presence of integrated BSV sequences in some banana cultivars which leads to false positives. In this study, a sequence-nonspecific, rolling-circle amplification (RCA) technique was developed and shown to overcome these limitations for the detection and subsequent characterization of BSV isolates infecting banana. This technique was shown to discriminate between integrated and episomal BSV DNA, specifically detecting the latter in several banana cultivars known to contain episomal or integrated sequences of Banana streak Mysore virus (BSMyV), Banana streak OL virus (BSOLV), and Banana streak GF virus (BSGFV). Using RCA, the presence of BSMyV and BSOLV was confirmed in Australia, while BSOLV, BSGFV, Banana streak Uganda I virus (BSUgIV), Banana streak Uganda L virus (BSUgLV), and Banana streak Uganda M virus (BSUgMV) were detected in Uganda. This is the first confirmed report of episomally-derived BSUglV, BSUgLV, and BSUgMV in Uganda. As well as its ability to detect BSV, RCA was shown to detect two other pararetroviruses, Sugarcane bacilliform virus in sugarcane and Cauliflower mosaic virus in turnip.

Ferromagnetic Resonance Biosensor for Homogeneous and Volumetric Detection of DNA

2017 ◽  
Author(s):  
Bo Tian ◽  
Peter Svedlindh ◽  
Mattias Strömberg ◽  
Erik Wetterskog
Keyword(s):  
Magnetic Nanoparticles ◽  
Ferromagnetic Resonance ◽  
Limit Of Detection ◽  
Point Of Care ◽  
Rolling Circle Amplification ◽  
Resonance Field ◽  
Isothermal Amplification ◽  
Detection Sensitivity ◽  
Serum Samples ◽  
Rolling Circle

In this work, we demonstrate for the first time, a ferromagnetic resonance (FMR) based homogeneous and volumetric biosensor for magnetic label detection. Two different isothermal amplification methods, <i>i.e.</i>, rolling circle amplification (RCA) and loop-mediated isothermal amplification (LAMP) are adopted and combined with a standard electron paramagnetic resonance (EPR) spectrometer for FMR biosensing. For RCA-based FMR biosensor, binding of RCA products of a synthetic Vibrio cholerae target DNA sequence gives rise to the formation of aggregates of magnetic nanoparticles. Immobilization of nanoparticles within the aggregates leads to a decrease of the net anisotropy of the system and a concomitant increase of the resonance field. A limit of detection of 1 pM is obtained with an average coefficient of variation of 0.16%, which is superior to the performance of other reported RCA-based magnetic biosensors. For LAMP-based sensing, a synthetic Zika virus target oligonucleotide is amplified and detected in 20% serum samples. Immobilization of magnetic nanoparticles is induced by their co-precipitation with Mg<sub>2</sub>P<sub>2</sub>O<sub>7</sub> (a by-product of LAMP) and provides a detection sensitivity of 100 aM. The fast measurement, high sensitivity and miniaturization potential of the proposed FMR biosensing technology makes it a promising candidate for designing future point-of-care devices.<br>

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