Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX

Barrio, Álvaro Martínez; Lagercrantz, Erik; Sperber, Göran; Blomberg, Jonas; Bongcam‐Rudloff, Erik

doi:10.1186/1471-2105-10-s6-s18

Cited by 22 publications

(2 citation statements)

References 34 publications

(33 reference statements)

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“…DNA sequences were aligned using Kalign (54) implemented in eBioX (55). Phylogenetic networks were constructed using SplitsTree4 (56) with Uncorrected_P characters transformation, and all gaps and repeat regions were excluded prior to analysis.…”

Section: Methodsmentioning

confidence: 99%

Recombination of Globally Circulating Varicella-Zoster Virus

Norberg

Depledge²,

Kundu³

et al. 2015

J Virol

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Varicella-zoster virus (VZV) is a human herpesvirus, which during primary infection typically causes varicella (chicken pox) and establishes lifelong latency in sensory and autonomic ganglia. Later in life, the virus may reactivate to cause herpes zoster (HZ; also known as shingles). To prevent these diseases, a live-attenuated heterogeneous vaccine preparation, vOka, is used routinely in many countries worldwide. Recent studies of another alphaherpesvirus, infectious laryngotracheitis virus, demonstrate that live-attenuated vaccine strains can recombine in vivo, creating virulent progeny. These findings raised concerns about using attenuated herpesvirus vaccines under conditions that favor recombination. To investigate whether VZV may undergo recombination, which is a prerequisite for VZV vaccination to create such conditions, we here analyzed 115 complete VZV genomes. Our results demonstrate that recombination occurs frequently for VZV. It thus seems that VZV is fully capable of recombination if given the opportunity, which may have important implications for continued VZV vaccination. Although no interclade vaccinewild-type recombinant strains were found, intraclade recombinants were frequently detected in clade 2, which harbors the vaccine strains, suggesting that the vaccine strains have already been involved in recombination events, either in vivo or in vitro during passages in cell culture. Finally, previous partial and complete genomic studies have described strains that do not cluster phylogenetically to any of the five established clades. The additional VZV strains sequenced here, in combination with those previously published, have enabled us to formally define a novel sixth VZV clade. IMPORTANCEAlthough genetic recombination has been demonstrated to frequently occur for other human alphaherpesviruses, herpes simplex viruses 1 and 2, only a few ancient and isolated recent recombination events have hitherto been demonstrated for VZV. In the present study, we demonstrate that VZV also frequently undergoes genetic recombination, including strains belonging to the clade containing the vOKA strain.

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Section: Methodsmentioning

confidence: 99%

Recombination of Globally Circulating Varicella-Zoster Virus

Norberg

Depledge²,

Kundu³

et al. 2015

J Virol

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“…The sequences used for designing primers are shown in Table 1. The sequences were aligned using eBioX 1.5.1 (Barrio, Lagercrantz, Sperber, Blomberg, & Bongcam-Rudloff, 2009), and we identified species-specific nucleotides for each species by eye. Primers with at least one speciesspecific site in the five nucleotides from the 3 0 ends with Tm values of around 60 C were selected.…”

Section: Designing Real-time Pcr Assaysmentioning

confidence: 99%

Real‐time polymerase chain reaction assays for environmental DNA detection of three salmonid fish in Hokkaido, Japan: Application to winter surveys

Minamoto

Hayami

Sakata

et al. 2018

Ecological Research

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Dolly Varden (Salvelinus malma) and Whitespotted Char (Salvelinus leucomaenis) are representative native fish of the family Salmonidae that inhabit the upper reaches of rivers on Hokkaido Island, Japan. They are threatened by the invasive Rainbow Trout (Oncorhynchus mykiss). In this study, environmental DNA (eDNA) real‐time polymerase chain reaction (PCR) assays to detect these three salmonids were developed and used to clarify the distribution pattern of these fish. A specificity test for each assay was conducted using DNA extracted from both target and closely related fish, and the specificity of each assay was confirmed. Then, we carried out eDNA surveys in two mountainous rivers around Mt. Daisetsu in winter, when snow depth was maximized. In the winter surveys, eDNA of all three species were successfully detected from river water samples, including under‐ice water samples. The results of eDNA detection corresponded with the results of an earlier distribution survey performed with Japanese‐style fly‐fishing and lure‐fishing. These results suggested that the eDNA assays developed in this study are applicable for inter‐seasonal surveys for these species.

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Consortium diversity of a sulfate‐reducing biofilm developed at acidic pH influent conditions in a down‐flow fluidized bed reactor

Montoya

Celis

Gallegos-García

et al. 2013

Engineering in Life Sciences

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Consortium diversity of a sulfate-reducing biofilm developed at acidic pH influent conditions in a down-flow fluidized bed reactorSulfate reduction is an appropriate approach for the treatment of effluents with sulfate and dissolved metals. In sulfate-reducing reactors, acetate may largely contribute to the residual organic matter, because not all sulfate reducers are able to couple the oxidation of acetate to the reduction of sulfate, limiting the treatment efficiency. In this study, we investigated the diversity of a bacterial community in the biofilm of a laboratory scale down-flow fluidized bed reactor, which was developed under sulfidogenic conditions at an influent pH between 4 and 6. The sequence analysis of the microbial community showed that the 16S rRNA gene sequence of almost 50% of the clones had a high similarity with Anaerolineaceae. At second place, 33% of the 16S rRNA phylotypes were affiliated with the sulfate-reducing bacteria Desulfobacca acetoxidans and Desulfatirhabdium butyrativorans, suggesting that acetotrophic sulfate reduction was occurring in the system. The remaining bacterial phylotypes were related to fermenting bacteria found at the advanced stage of reactor operation. The results indicate that the acetotrophic sulfate-reducing bacteria were able to remain within the biofilm, which is a significant result because few natural consortia harbor complete oxidizing sulfate-reducers, improving the acetate removal via sulfate reduction in the reactor.

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Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX

Cited by 22 publications

References 34 publications

Recombination of Globally Circulating Varicella-Zoster Virus

Recombination of Globally Circulating Varicella-Zoster Virus

Real‐time polymerase chain reaction assays for environmental DNA detection of three salmonid fish in Hokkaido, Japan: Application to winter surveys

Consortium diversity of a sulfate‐reducing biofilm developed at acidic pH influent conditions in a down‐flow fluidized bed reactor

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