Traces of ATCV-1 associated with laboratory component contamination

Kjartansdóttir, Kristín Rós; Friis-Nielsen, Jens; Asplund, Maria E.; Mollerup, Sarah; Mourier, Tobias; Jensen, Randi Holm; Hansen, Thomas Arn; Rey‐Iglesia, Alba; Richter, Stine Raith; Olsen, Pernille V. S.; Vinner, Lasse; Fridholm, Helena; Sicheritz-Pontén, Thomas; Nielsen, Lars Peter; Brunak, Søren; Willerslev, Eske; Izarzugaza, Jose M. G.; Hansen, Anders J.

doi:10.1073/pnas.1423756112

Cited by 24 publications

(16 citation statements)

References 5 publications

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“…The specific origin of the contaminating viruses in our study was not clear although some avian herpesviruses were only linked to the QIA extracts. The ubiquitous presence of contaminating viruses stress the importance of including negative controls in future viral metagenomics studies, as well as adding measures to reduce the problem [55,56]. …”

Section: Discussionmentioning

confidence: 99%

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

et al. 2017

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Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult. Current studies have tackled these challenges in many different ways employing a wide range of viral concentration and extraction procedures. However, there is limited knowledge of the efficacy and inherent biases associated with these methods in respect to viral sewage metagenomics, hampering the development of this field. By the use of next generation sequencing this study aimed to evaluate the efficiency of four commonly applied viral concentrations techniques (precipitation with polyethylene glycol, organic flocculation with skim milk, monolithic adsorption filtration and glass wool filtration) and extraction methods (Nucleospin RNA XS, QIAamp Viral RNA Mini Kit, NucliSENS® miniMAG®, or PowerViral® Environmental RNA/DNA Isolation Kit) to determine the viriome in a sewage sample. We found a significant influence of concentration and extraction protocols on the detected viriome. The viral richness was largest in samples extracted with QIAamp Viral RNA Mini Kit or PowerViral® Environmental RNA/DNA Isolation Kit. Highest viral specificity were found in samples concentrated by precipitation with polyethylene glycol or extracted with Nucleospin RNA XS. Detection of viral pathogens depended on the method used. These results contribute to the understanding of method associated biases, within the field of viral sewage metagenomics, making evaluation of the current literature easier and helping with the design of future studies.

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Section: Discussionmentioning

confidence: 99%

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

et al. 2017

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“…That virus is known to infect endosymbiotic algae of the protist Acanthocystis turfacea, 452 and some reports suggest that it may also infect mammalian hosts [94], suggesting a 453 broad tropism. Though still disputed [95,96], this observation could suggest that 454 Branchiostoma may also be sensitive to that virus. Yet, for this potential pathogen too, 455 detected small RNA reads fail to display any size or sequence bias: they do not appear 456 to be siRNAs (see Supplementary File S1, section 10).…”

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confidence: 97%

Functional lability of RNA-dependent RNA polymerases in animals

Pinzón

Bertrand²,

Subirana³

et al. 2018

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RNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more common in animals than previously thought, even in insects, where they had been assumed not to exist. RdRP genes were present in the ancestors of numerous clades, and they were subsequently lost at a high frequency. In order to probe the function of RdRPs in a deuterostome (the cephalochordate Branchiostoma lanceolatum), we performed high-throughput analyses of small RNAs from various Branchiostoma developmental stages. Our results show that Branchiostoma RdRPs do not appear to participate in RNAi: we did not detect any candidate small RNA population exhibiting classical siRNA length or sequence features. Our results show that RdRPs have been independently lost in dozens of animal clades, and even in a clade where they have been conserved (cephalochordates) their function in RNAi amplification is not preserved. Such a dramatic functional variability reveals an unexpected plasticity in RNA silencing pathways. Author summaryRNA interference (RNAi) is a conserved gene regulation system in eukaryotes. In non-animal eukaryotes, it necessitates RNA-dependent RNA polymerases ("RdRPs"). Among animals, only nematodes appear to require RdRPs for RNAi. Yet additional animal clades have RdRPs and it is assumed that they participate in RNAi. Here, we find that RdRPs are much more common in animals than previously thought, but their genes were independently lost in many lineages. Focusing on a species with RdRP genes (a cephalochordate), we found that it does not use them for RNAi. While RNAi is the only known function for eukaryotic RdRPs, our results suggest additional roles. Eukaryotic RdRPs thus have a complex evolutionary history in animals, with frequent independent losses and apparent functional diversification. November 28, 2018 1/23 Phylogenetic tree reconstruction 100 Amino acid sequences of the eukaryotic RdRP domain (Pfam #PF05183) were retrieved 101 from PFAM [35], and supplemented with the RdRP domains of the proteins identified 102 in the 538 animal proteomes (cf above). Sequences were aligned using hmmalign [36] 103 using the HMM profile of the PF05183 RdRP domain. Sequences for which the domain 104 was incomplete were deteled from the alignment. Sites used to reconstruct the 105 phylogenetic tree were selected using trimAl [37] on the Phylemon 2.0 webserver [38]. 106 Bayesian inference (BI) tree was inferred using MrBayes 3.2.6 [39], with the model 107 recommended by ProtTest 1.4 [40] under the Akaike information criterion (LG+Γ), at 108 the CIPRES Science Gateway portal [41]. Two independent runs were performed, each 109 with 4 chains and one million generations. A burn-in of 25% was used and a fifty 110 majority-rule consensus tree was calculated for the remaining ...

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“…These authors determined that chlorovirus ATCV‐1, a previously unrecognized algal virus, was associated with decreased cognitive performance in humans. Interestingly, feeding of ATCV‐1 infected algae to mice for 6 weeks caused impaired cognition and changes in hippocampal genes compatible with cognitive impairment (but also see correspondence and comments about this paper (Kjartansdottir et al ., ; Yolken et al ., ).…”

Section: Hyposmiamentioning

confidence: 98%

Disruptive physiology: olfaction and the microbiome–gut–brain axis

2017

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This review covers the field of olfaction and chemosensation of odorants and puts this information into the context of interactions between microbes and behaviour; the microbiome-gut-brain axis (MGBA). Recent emphasis has also been placed on the concept of the holobiome which states that no single aspect of an organism should be viewed separately and thus must include examination of their associated microbial populations and their influence. While it is known that the microbiome may be involved in the modulation of animal behaviour, there has been little systematized effort to incorporate into such studies the rapidly developing knowledge of the wide range of olfactory systems. The classical olfactory system is evolutionarily conserved in multiple taxa from insects through to fish, reptiles and mammals, and is represented by the largest gene families in vertebrates. Mice have over 1000 different olfactory receptors and humans about 400. They are distributed throughout the body and are even found in spermatozoa where they function in chemotaxis. Each olfactory receptor has the unique functional capability of high-affinity binding to several different molecular ligands. These and other properties render the cataloguing of odorants (odorome) with specific actions a difficult task. Some ectopic olfactory receptors have been shown to have functional effects in the gut and kidney, highlighting the complexity of the systems engaged by odorants. However, there are, in addition to classical olfactory receptors, at least two other families of receptors involved in olfaction that are also widely found expressed on tissues in many different organs in addition to the nervous system and brain: the trace-amine associated and formyl peptide receptors. Bacteria can make many if not most odorants and are responsible for recognition of species and relative relatedness, as well as predator presence, among many other examples. Activation of different combinations of olfactory receptors by bacterial products such as β-phenylethylamine have been shown even to control expression of emotions such as fear and aggression. The number of examples of bacterial products and volatile odorants influencing brain function and behaviour is expanding rapidly. Since it is recognized that many different bacterial products and metabolites also function as social cues, and may themselves be directly or indirectly causative of behavioural change, it becomes ever more important to include olfaction into studies of the MGBA. Clearly there are broader implications for the involvement of olfaction in this rapidly evolving field. These include improvement in our understanding of the pathways engaged in various behaviours, and the identification of novel approaches and new targets in efforts to modulate behavioural changes.

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Traces of ATCV-1 associated with laboratory component contamination

Cited by 24 publications

References 5 publications

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

Functional lability of RNA-dependent RNA polymerases in animals

Disruptive physiology: olfaction and the microbiome–gut–brain axis

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