Plasmonic Silver Nanoparticle-Impregnated Nanocomposite BiVO₄ Photoanode for Plasmon-Enhanced Photocatalytic Water Splitting

Herein, we developed a fully solution-deposited nanocomposite photoanode based on silver nanoparticle (NP)-impregnated bismuth vanadate (BiVO₄) films. The synthesized Ag NPs exhibit diameters of few nanometers and uniform matrix dispersion, which were confirmed by high-resolution transmission electron microscopy. The photoanode composed of the Ag NP-incorporated nanocomposite BiVO₄ showed a remarkable enhancement in both low potential and the saturated photocatalytic current densities in comparison with the pristine BiVO₄ film. The observed experimental results are attributed to the improved carrier generation and enhanced charge separation by the localized surface plasmon resonance-mediated effect as suggested by electrochemical impedance spectroscopy and a numerical simulation

RNA-Seq Approach for Genetic Improvement of Meat Quality in Pig and Evolutionary Insight into the Substrate Specificity of Animal Carbonyl Reductases

<div><p>Changes in meat quality traits are strongly associated with alterations in postmortem metabolism which depend on genetic variations, especially nonsynonymous single nucleotide variations (nsSNVs) having critical effects on protein structure and function. To selectively identify metabolism-related nsSNVs, next-generation transcriptome sequencing (RNA-Seq) was carried out using RNAs from porcine liver, which contains a diverse range of metabolic enzymes. The multiplex SNV genotyping analysis showed that various metabolism-related genes had different nsSNV alleles. Moreover, many nsSNVs were significantly associated with multiple meat quality traits. Particularly, <em>ch7:g.22112616A>G</em> SNV was identified to create a single amino acid change (Thr/Ala) at the 145th residue of H1.3-like protein, very close to the putative 147th threonine phosphorylation site, suggesting that the nsSNV may affect multiple meat quality traits by affecting the epigenetic regulation of postmortem metabolism-related gene expression. Besides, one nonsynonymous variation, probably generated by gene duplication, led to a stop signal in porcine testicular carbonyl reductase (PTCR), resulting in a C-terminal (E281-A288) deletion. Molecular docking and energy minimization calculations indicated that the binding affinity of wild-type PTCR to 5α-DHT, a C₂₁-steroid, was superior to that of C-terminal-deleted PTCR or human carbonyl reductase, which was very consistent with experimental data, reported previously. Furthermore, P284 was identified as an important residue mediating the specific interaction between PTCR and 5α-DHT, and phylogenetic analysis showed that P284 is an evolutionarily conserved residue among animal carbonyl reductases, which suggests that the C-terminal tails of these reductases may have evolved under evolutionary pressure to increase the substrate specificity for C₂₁-steroids and facilitate metabolic adaptation. Altogether, our RNA-Seq revealed that selective nsSNVs were associated with meat quality traits that could be useful for successful marker-assisted selection in pigs and also represents a useful resource to enhance understanding of protein folding, substrate specificity, and the evolution of enzymes such as carbonyl reductase.</p> </div

Comparison of the 5α-DHT binding mode among wild-type and C-terminal-deleted PTCRs and human carbonyl reductase.

<p>(A) The final conformation of wild-type PTCR (blue, PDB ID: 1N5D) bound with NADPH (yellow) and 5α-DHT substrate (dark pink). The structure contains a C-terminal tail (red, E281-A288). (B) The final conformation of C-terminal-deleted PTCR docked with 5α-DHT. (C) The final conformation of human carbonyl reductase (green, PDB ID: 1WMA) docked with 5α-DHT. (D) Detailed binding mode of 5α-DHT with wild-type PTCR is highlighted by a box in panel (A). Hydrogen bond interactions are represented by blue lines. (E) Detailed binding mode of 5α-DHT with C-terminal-deleted PTCR is highlighted by a box in panel (B). (F) Detailed binding mode of 5α-DHT with human carbonyl reductase is highlighted by a box in panel (C).</p

Hydrophobic and hydrogen bond interaction profiles.

<p>Hydrophobic and hydrogen bond interaction profiles.</p

Summary of SNV candidates obtained by RNA-seq.

a<p>SNV candidates were identified according to information in the UniGene database.</p>b<p>ORF: open reading frame.</p>c<p>Non-identified SNVs: SNV candidates that have not been identified in the UniGene database.</p>d<p>Total SNV candidates: the sum of identified and non-identified SNV candidates.</p

Phylogenetic comparison of PTCR homologs from various organisms.

<p>(A) Phylogenetic tree of PTCR homologs. The phylogenetic tree was constructed using the neighbor-joining method and visualized using MEGA4 software. GenBank accession numbers of PTCR homologs are as follows: catfish (ADO28395), cattle (NP_001030258), chicken (NP_001025966), chimpanzee (XP_531449), dog (XP_535589), finch (XP_002187585), hamster (BAB62840), horse (XP_001493595), human (NP_001748), macaque (BAB97216), marmoset (XP_002761453), mouse (NP_031646), pig (NP_999238), rabbit (NP_001076218), rat (NP_062043), salmon (ACI69439), and trout (NP_001118068). Asterisks indicate carbonyl reductases possessing the additional C-terminal tail. (B) Alignment of the amino acid sequences of a C-terminal segment of PTCR homologs in (A). The box indicates additional C-terminal tails. The arrow represents the residue that mutated nonsynonymously into a stop signal in PTCR. The asterisk represents the proline residues conserved among pig, dog, horse, and cattle.</p

Functional classification of genes containing nonsynonymous SNV candidates.

<p>A total of 229 genes were found to include the 580 nonsynonymous SNV candidates shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042198#pone-0042198-t001" target="_blank">Table 1</a>. In addition, they were further classified according to function. The vertical axis on the graph (“No. of gene”) represents the total number of genes.</p

Summary of the significant associations between nsSNVs and meat quality traits.

a<p>Meat quality traits include carcass weight (CW), backfat thickness (BFT), meat color (lightness, CIE <i>L</i>; redness, CIE <i>a</i>; yellowness, CIE <i>b</i>), cooking loss (CW), drip loss (DL), chemical compositions (protein, Pro; fat, Fat; collagen, Coll; moisture, Moi), shear force (SF), water holding capacity (WHC), and postmortem pH (pH_{24 hr}; pH_{45 min}).</p>b<p>SNV location is based on the pig genome assembly (SGSC Sscrofa9.2/susScr2). The triangle (▵) and circle (○) represent significant differences (▵, p<0.05; ○, p<0.01) in genotypes under a codominant model.</p

List of nsSNVs validated in porcine liver genes using RNA-Seq and a genotyping assay.

<p>nsSNVs, identified by RNA-Seq, were validated by Illumina VeraCode GoldenGate genotyping.</p>a<p>SNV location is based on the pig genome assembly (SGSC Sscrofa9.2/susScr2).</p>b<p>Nonsyn represents nonsynonymous variation, leading to the change of an amino acid.</p>c,d<p>Minor allele frequency and χ²-test <i>p</i> value for Hardy–Weinberg equilibrium, respectively.</p