Water Footprint Assessment for Wastewater Treatment: Method, Indicator, and Application

The water footprint in terms of the sum of both direct and indirect water cost of wastewater treatment is for the first time accounted in this work. On the basis of the hybrid method as a combination of process analysis and input–output analysis, a detailed water footprint accounting procedure is provided to cover the supply chain of a wastewater treatment plant. A set of indices intending to reveal the efficiency as well as renewability of wastewater treatment systems are devised as parallels of corresponding indicators in net energy analysis for energy supply systems. A case study is carried out for the Beijing Space City wastewater treatment plant as a landmark project. The high WROI (water return on investment) and low WIWP (water investment in water purified) indicate a high efficiency and renewability of the case system, illustrating the fundamental function of wastewater treatment for water reuse. The increasing of the wastewater and sludge treatment rates are revealed in an urgent need to reduce the water footprint of China and to improve the performance of wastewater treatment

Upregulated genes.

<p>Upregulated genes.</p

Tandem duplications lead to novel expression patterns through exon shuffling in <i>Drosophila yakuba</i>

<div><p>One common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes. Here, we use genome wide RNA-seq data from a population sample of <i>Drosophila yakuba</i> to test this ‘gene dosage’ hypothesis. We observe little evidence of expression changes in response to whole transcript duplication capturing 5′ and 3′ UTRs. Among whole gene duplications, we observe evidence that dosage sharing across copies is likely to be common. The lack of expression changes after whole gene duplication suggests that the majority of genes are subject to tight regulatory control and therefore not sensitive to changes in gene copy number. Rather, we observe changes in expression level due to both shuffling of regulatory elements and the creation of chimeric structures via tandem duplication. Additionally, we observe 30 <i>de novo</i> gene structures arising from tandem duplications, 23 of which form with expression in the testes. Thus, the value of tandem duplications is likely to be more intricate than simple changes in gene dosage. The common regulatory effects from chimeric gene formation after tandem duplication may explain their contribution to genome evolution.</p></div

Expression levels (in FPKM) for unduplicated ancestral state for three <i>D. yakuba</i> reference replicates for genes that are duplicated in sample strains compared to expression levels for all genes.

<p>FPKM values are indicative of ancestral expression patterns prior to duplication. Duplicated genes have higher mean and median ancestral expression compared to non-duplicated genes in female tissues (A) and male tissues (B). Genes that are duplicated have lower median expression in ovary compared to carcass in females (A) but there is no difference in expression in reproductive vs. somatic tissue in males (B). Plots shown exclude outliers.</p

Mean fold change in sample strains vs. reference for strains containing chimeras or whole gene duplicates (red) and unmutated sample strains for the same regions (grey) in A) ovaries B) female carcass C) testes D) male carcass.

<p>Chimeric genes are more likely to result in high mean fold change than unmutated counterparts in all tissues. Whole gene duplicates create multifold expression changes more rarely.</p

Chimeric gene structures result in novel expression patterns.

<p>A tandem duplication that does not respect gene boundaries unites the 5′ end of <i>GE18453</i> with the 3′ end of <i>GE18451</i> to produce a chimeric gene on chromosome 2L. Plot shows quantile normalized coverage in RNA seq data for sample (red) and reference (grey) with HMM output (blue) on chromosome 2L for female carcass. The chimera displays a change in transcript levels, while transcript levels for parental gene sequence are not altered. Sites with upregulated or downregulated sequence as defined by HMM output is shown in blue, using the right axis. HMM state calls for sites with unchanged expression are not shown. The region spanned by the tandem duplication is shaded in grey. The region spanned by the chimeric gene shows high-level upregulation. The whole gene duplication of <i>GE18452</i> does not display a significant change in mRNA levels but rather falls within the bounds of expression profiles for reference replicates (Ref FPKM = 19.9; Sample FPKM = 24.5; uncorrected <i>P</i> = 0:52; corrected <i>P</i> = 1:0).</p

Duplication followed by secondary deletion, as indicated by a total of 104 long-spanning read pairs, leads to an expression change in a gene fragment of <i>GE21202</i> on chromosome 3L.

<p>Plot shows normalized coverage in RNA seq data for sample (red) and reference (grey) with HMM output (blue) on chromosome 3L. Only the sample strain with the deletion shows such upregulation. Transcript levels increase by greater than two-fold, beyond changes that would be produced by additive changes in gene dosage. Sites with upregulated or downregulated sequence as defined by HMM output is shown in blue, using the right axis. HMM state calls for sites with unchanged expression are not shown. HMM output for upregulated regions match well with the predicted gene structures formed by this complex mutation. The region spanned by the tandem duplication is shaded in grey.</p

Tandem duplication creates a <i>de novo</i> gene on chromosome 3R.

<p>The 5′ end of GE24349 is duplicated and placed adjacent to formerly untranscribed sequence, producing transcription and putative <i>de novo</i> gene creation. The reference strain does not show transcription in the region (grey) and no other sample strain exhibits upregulated sequence across the region. Sites with upregulated or downregulated sequence as defined by HMM output is shown in blue, using the right axis. HMM state calls for sites with unchanged expression are not shown. The region spanned by the tandem duplication is shaded in grey. The tandem duplication activates a previously untranscribed region from roughly 14703500–14705000 bp. There is also upregulation in some exons for <i>GE24349</i>, possibly indicating a longer fusion transcript that reads through to the end of the nearest adjacent 3′ UTR.</p

Intracellular distribution of NS80 C-terminal truncations in transfected cells.

<p>Vero cells were transfected with plasmids expressing the NS80 or its C-terminal truncations. At 18 h p.t., cells were fixed and immunostained with corresponding antibodies. Nuclei were stained blue with DAPI.</p

Viral inclusions formed in NS80 singly transfected cells.

<p>CIK monolayers were transfected with NS80-expressing plasmid, and then fixed at different times p.t. for immunostaining. Nuclei were stained with DAPI (blue). <b>A</b>. Time course distribution of NS80 in transfected CIK cells. The cells were fixed at 6 h, 12 h, 18 h, and 24 h p.t respectively and immunostained with rabbit anti-NS80 serum and then with FITC-conjugated goat anti-rabbit IgG (green). <b>B</b>. Ubiquitination analysis of expressed NS80 protein. The cells were fixed at 12 h and 24 h p.t. and then immunostained with corresponding antibodies.</p