Viruses Detection in a Wild Plant, Arctium tomentosum, by siRNA Deep-Sequencing

Plant is able to recognize dsRNA, and cleave the dsRNA into siRNA in the cell. This mechanism helps plant to against virus. A novel method of virus detection based on siRNA deep-sequencing has been developed. The method does not require any prior supposition, and it provides an unbiased view for detecting of all viruses. Thus it was used to detect viruses from a wild plant (Arctium tomentosum) with viral symptoms in Helsinki, Finland. Overlapping siRNA reads were used to build contigs using the program Velvet. Programs MAQ and Novoalign were used to align the siRNA reads to a reference sequence for the viral sequence recovery. In this study, two viruses, Alstroemeria virus X (AlsVX, genus Potexvirus, family Alphaflexiviridae) and Fig mosaic virus-Hel (FMV, unassigned genus Emaravirus) were identified. This is the first report for the occurrences of both viruses in Finland. The siRNA deep-sequencing detection results were confirmed by RT-PCR. The distributions of the viruses in Helsinki were also studied. Partial sequences of AlsVX-Hel and FMV-Hel were compared with related viruses in NCBI. The amino acid identity of the coat protein gene between AlsVX-Hel detected from Helsinki and AlsVX-Jap from Japan is 90%, and the amino acid identities of the putative nucleocapsid protein gene between FMV-Hel and other FMV strains were about 78%. The differences indicate that the AlsVX-Hel in Helsinki might be a new strain of AlsVX, and FMV-Hel might be a new strain of FMV, or a new virus

Soil Storage Conditions Alter the Effects of Tire Wear Particles on Microbial Activities in Laboratory Tests

In this study, we focused on the fact that soil storage conditions in the laboratory have never been considered as a key factor potentially leading to high variation when measuring effects of microplastics on soil microbial activity. We stored field-collected soils under four different conditions [room-temperature storage, low-temperature storage (LS), air drying (AD), and heat drying] prior to the experiment. Each soil was treated with tire wear particles (TWPs), and soil microbial activities and water aggregate stability were investigated after soil incubation. As a result, microbial activities, including soil respiration and three enzyme activities (β-glucosidase, N-acetyl-β-glucosaminidase, and phosphatase), were shown to depend on soil storage conditions. Soil respiration rates increased with the addition of TWPs, and the differences from the control group (no TWPs added) were more pronounced in the AD TWP treatment than in soils stored under other conditions. In contrast, phosphatase activity followed an opposing trend after the addition of TWPs. The AD soil had higher phosphatase activity after the addition of TWPs, while the LS soil had a lower level than the control group. We suggest that microplastic effects in laboratory experiments can strongly depend on soil storage conditions

Small-RNA Deep Sequencing Reveals Arctium tomentosum as a Natural Host of Alstroemeria virus X and a New Putative Emaravirus

Peer reviewe

Phylogenetic analysis of partial putative nucleocapsid protein (NP) gene sequences (518 nt; RNA3) of established and putative members of genus <i>Emaravirus</i>.

<p>The NP gene sequence of <i>Pigeonpea sterility mosaic virus</i> is not available and could not be included. Bootstrap values higher than 80 (of 100 replicates) are indicated on the branches. For accession numbers, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042758#pone-0042758-t001" target="_blank">Table 1</a>. Bar indicates 0.1 Kimura units <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042758#pone.0042758-Kimura1" target="_blank">[34]</a>.</p

Percentage nucleotide (518 nt; upper triangle) and deduced amino acid identities (lower triangle) of the nucleocapsid protein gene of WBYVV and related negative-strand ssRNA viruses (see Table 1 for sequence accession numbers).

<p>Percentage nucleotide (518 nt; upper triangle) and deduced amino acid identities (lower triangle) of the nucleocapsid protein gene of WBYVV and related negative-strand ssRNA viruses (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042758#pone-0042758-t001" target="_blank">Table 1</a> for sequence accession numbers).</p

Viral sequences obtained from public databases and used in the study.

a<p>The CP (AlsVX) or partial NP gene sequence (WBYVV) was determined in this study by amplification of the viral genomic region using RT-PCR and sequencing of the products.</p>b<p>Established and putative members of the genus.</p

Percentage nucleotide (upper triangle) and deduced amino acid identities (lower triangle) of the coat protein genes of three isolates of <i>Alstroemeria virus X</i> and other potexviruses (see Table 1 for sequence accession numbers).

<p>Percentage nucleotide (upper triangle) and deduced amino acid identities (lower triangle) of the coat protein genes of three isolates of <i>Alstroemeria virus X</i> and other potexviruses (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042758#pone-0042758-t001" target="_blank">Table 1</a> for sequence accession numbers).</p

Leaves of woolly burdock (<i>A. tomentosum</i>) plants with and without virus-like symptoms.

<p>Plants Vi4, Vi5 and Vi8 (orange labels) were infected with WBYVV and the leaves display vein yellowing and mosaic symptoms. Plants were photographed in the Viikki Research Farm area on May 18, 2011.</p

Dimensional Analysis Model of Head Loss for Sand Media Filters in a Drip Irrigation System Using Reclaimed Water

A new model was developed to predict head loss in sand media filters. Sand filters with six different media using reclaimed water were used to measure head losses at different flow rates in the laboratory. The parameters influencing head losses were considered to be the uniformity coefficient, the effective diameter, the sand mass, the filtration velocity, the pollution load, and the water viscosity. A dimensional analysis method was used to develop the model. A comparison between the predicted and the measured head losses showed close agreement with a correlation coefficient of 91.7%, reaching a significance level of p < 0.001. The results showed that the model might give satisfactory predictions within the following range of operational and filter structure parameters: uniformity coefficient 1.48–3.31; effective diameter 0.41–2.1 mm; pollution load 0.0169–4.2049 kg, filtration velocity 0.0038–0.0398 m/s

Ternary hierarchical structure based solar‐driven evaporator for long‐lasting concentrated brine treatment

Abstract Solar‐driven evaporation has been a promising desalination method for treating concentrated seawater, since it is cost‐effectiveness, simplicity, and environmentally friendly. However, this method faces an unavoidable long‐term problem that the salt generated in the evaporation processes would affect and hinder its evaporation efficiency. Because the salt inevitably crystallizes on the surface of photothermal evaporation materials, and this crystallization process increases with time to impair the material area of the sunlight absorption and evaporation. Here, we show a ternary hierarchical structure based solar‐driven evaporator that reduces the evaporation material surface coverage of the salt to get long‐lasting concentrated brine treatment capacity. This evaporator is constructed by plugging vertically arranged hollow tube arrays across a porous plate. The top, middle, and bottom of the evaporator respectively serve as the salt crystallization site, the evaporation site, and the light absorption site. Meanwhile, the self‐cleaning of the evaporator can be achieved by back diffusion of the crystallized salts. As a result, this efficient and durable evaporator exhibits freshwater production of 10.21 kg/(m2·day) in outdoor experiment in the treatment of the concentrated natural seawater (21.3 wt%)