Molecular Modifications and Control of Processes to Facilitate the Synergistic Degradation of Polybrominated Diphenyl Ethers in Soil by Plants and Microorganisms Based on Queuing Scoring Method.

In this paper, a combination of modification of the source and regulation of the process was used to control the degradation of PBDEs by plants and microorganisms. First, the key proteins that can degrade PBDEs in plants and microorganisms were searched in the PDB (Protein Data Bank), and a molecular docking method was used to characterize the binding ability of PBDEs to two key proteins. Next, the synergistic binding ability of PBDEs to the two key proteins was evaluated based on the queuing integral method. Based on this, three groups of three-dimensional quantitative structure-activity relationship (3D-QSAR) models of plant-microbial synergistic degradation were constructed. A total of 30 PBDE derivatives were designed using BDE-3 as the template molecule. Among them, the effect on the synergistic degradation of six PBDE derivatives, including BDE-3-4, was significantly improved (increased by more than 20%) and the environment-friendly and functional evaluation parameters were improved. Subsequently, studies on the synergistic degradation of PBDEs and their derivatives by plants and microorganisms, based on the molecular docking method, found that the addition of lipophilic groups by modification is beneficial to enhance the efficiency of synergistic degradation of PBDEs by plants and microorganisms. Further, while docking PBDEs, the number of amino acids was increased and the binding bond length was decreased compared to the template molecules, i.e., PBDE derivatives could be naturally degraded more efficiently. Finally, molecular dynamics simulation by the Taguchi orthogonal experiment and a full factorial experimental design were used to simulate the effects of various regulatory schemes on the synergistic degradation of PBDEs by plants and microorganisms. It was found that optimal regulation occurred when the appropriate amount of carbon dioxide was supplied to the plant and microbial systems. This paper aims to provide theoretical support for enhancing the synergistic degradation of PBDEs by plants and microorganisms in e-waste dismantling sites and their surrounding polluted areas, as well as, realize the research and development of green alternatives to PBDE flame retardants.

Genome-wide identification, evolution, and expression analysis of RNA-binding glycine-rich protein family in maize.

The RNA-binding glycine-rich protein (RB-GRP) family is characterized by the presence of a glycine-rich domain arranged in (Gly)n-X repeats and an RNA-recognition motif (RRM). RB-GRPs participate in varied physiological and biochemical processes especially in the stress response of plants. In this study, a total of 23 RB-GRPs distributed on 10 chromosomes were identified in maize (Zea mays L.), and they were divided into four subgroups according to their conserved domain architecture. Five pairs of paralogs were identified, while none of them was located on the same chromosomal region, suggesting that segmental duplication is predominant in the duplication events of the RB-GRPs in maize. Comparative analysis of RB-GRPs in maize, Arabidopsis (Arabidopsis thaliana L.), rice (Oryza sativa L.), and wheat (Triticum aestivum) revealed that two exclusive subgroups were only identified in maize. Expression of eight ZmRB-GRPs was significantly regulated by at least two kinds of stresses. In addition, cis-elements predicted in the promoter regions of the ZmRB-GRPs also indicated that these ZmRB-GRPs would be involved in stress response of maize. The preliminary genome-wide analysis of the RB-GRPs in maize would provide useful information for further study on the function of the ZmRB-GRPs.

Process-specified emission factors and characteristics of VOCs from the auto-repair painting industry.

Daily use of passenger vehicles leads to considerable emission of volatile organic compounds (VOCs), which are key precursors to the ground-level ozone pollution. While evaporative and tailpipe emission of VOCs from the passenger vehicles can be eliminated largely, or even completely, by electrification, VOCs emission from the use of coatings in auto-repair is unavoidable and has long been ignored. Here, we present for the first time, to the best of our knowledge, a comprehensive investigation on the emission factors and process-specified characteristics of VOCs from auto-repair painting, based on field measurements over 15 representative auto-repair workshops in the Pearl-River-Delta area, China. Replacement of solvent-borne coatings with water-borne counterparts, which was only achieved partially in the Basecoat step but not in the Putty, Primer and Clearcoat steps, could reduce the per automobile VOCs emission from 756.5 to 489.6 g and the per automobile ozone formation potential (OFP) from 2776.5 to 1666.4 g. Implementation of exhaust after-treatment led to a further reduction of the per automobile VOCs emission to 340.9 g, which is still ca. 42% higher than that from the state-of-art painting processes for the manufacture of passenger vehicles. According to the analysis of VOCs compositions, the Putty process was dominated by the emission of styrene, while Primer, Basecoat (solvent-borne) and Clearcoat steps were all characterized by the emission of n-butyl acetate and xylenes. By contrast, water-borne Basecoat step showed a prominent emission of n-amyl alcohol. Notably, for the full painting process to repair an automobile, n-butyl acetate emerged as the most abundant species in the VOCs emission, whereas xylenes contributed most significantly to the OFP. Scenario analysis suggested that reducing VOCs contents in the coatings, as well as improving the after-treatment efficiency, were highly potential solutions for effective reduction of VOCs emission from auto-repair. Our study contributes to an update of industrial inventories of VOCs emission, and may provide valuable insights for reducing VOCs emission and OFPs from the auto-repair industry.

Generation and immunogenicity of Japanese encephalitis virus envelope protein expressed in transgenic rice.

Transgenic plants have become attractive as bioreactors to produce heterologous proteins that can be developed as edible vaccines. In the present study, transgenic rice expressing the envelope protein (E) of Japanese encephalitis virus (JEV), under the control of a dual cauliflower mosaic virus (CaMV 35S) promoter, was generated by Agrobacterium-mediated transformation. Southern blot, Northern blot, Western blot and ELISA analyses confirmed that the E gene was integrated into transgenic rice and was expressed in the leaves at levels of 1.1-1.9 microg/mg of total soluble protein. After intraperitoneal immunization of mice with crude protein extracts from transgenic rice plants, JEV-specific neutralizing antibody could be detected. Moreover, E-specific mucosal immune responses could be detected in mice after oral immunization with protein extracts from transgenic rice plants. These results show the potential of using a transgenic rice-based expression system as an alternative bioreactor for JEV subunit vaccine.

Functional divergence and origin of the DAG-like gene family in plants.

The nuclear-encoded DAG-like (DAL) gene family plays critical roles in organelle C-to-U RNA editing in Arabidopsis thaliana. However, the origin, diversification and functional divergence of DAL genes remain unclear. Here, we analyzed the genomes of diverse plant species and found that: DAL genes are specific to spermatophytes, all DAL genes share a conserved gene structure and protein similarity with the inhibitor I9 domain of subtilisin genes found in ferns and mosses, suggesting that DAL genes likely arose from I9-containing proproteases via exon shuffling. Based on phylogenetic inference, DAL genes can be divided into five subfamilies, each composed of putatively orthologous and paralogous genes from different species, suggesting that all DAL genes originated from a common ancestor in early seed plants. Significant type I functional divergence was observed in 6 of 10 pairwise comparisons, indicating that shifting functional constraints have contributed to the evolution of DAL genes. This inference is supported by the finding that functionally divergent amino acids between subfamilies are predominantly located in the DAL domain, a critical part of the RNA editosome. Overall, these findings shed light on the origin of DAL genes in spermatophytes and outline functionally important residues involved in the complexity of the RNA editosome.

Expression analysis of orf77 and R region in mitochondrial DNA of S-type CMS maize.

It is generally recognized that S type of CMS in maize associated with the recombination region R in mitochondria. Complicated DNA recombination and changes of transcripts of R are observed in several subgroups of S cytoplasm. R region includes two open reading frames (orf355 and orf77) and they are all chemeric. Among the sequence of orf77, there are three stretches similar to atp9 of mitochondria. Many different S cytoplasms are found in maize in China and researches on them show that similar R region and sequence are also found in the mitochondrial DNA in Tangxu, Shuang and J (cytoplasm. Northern analysis of Tangxu, J cytoplasm with Probe R and orf77 indicates that orf77 co-transcribes with R region and the nuclear restorer gene Rf3 affects their expression. In all tested S cytoplasm plants with the genotype of s-rf3rf3, both probe orf77 and R can detect six transcripts of 2.8, 1.6, 1.1, 0.9, 0.7 and 0.4 kb. In the presence of the nuclear restorer-of-fertility gene Rf3, previous transcripts of 2.8 kb and 1.6 kb are disappeared, but the other four transcripts are not changed. In T and C cytoplasm of CMS, only four transcripts of 1.1, 0.9, 0.7 and 0.4 kb appear when hybrid to probe R. Further Northern analysis of probe atp9 proved that all the four transcripts of 1.1, 0.9, 0.7 and 0.4 kb were actually transcripts of gene atp9, so only the transcripts of 2.8 kb and 1.6 kb are particular to R region of S. In addition, atp9, atp6 and cox II each has the same transcription pattern in tassel with different genotypes respectively. It can be included that R region and orf77 are the most important candidate gene for S-CMS.

The 5' stem-loop and its role in mRNA stability in maize S cytoplasmic male sterility.

The co-transcribed orf355-orf77 region of the mitochondrial genome is associated with S cytoplasmic male sterility (CMS-S) in maize; the amounts of its 1.6- and 2.8-kb transcripts were previously shown to be greatly reduced in fertility-restored microspores relative to the amounts in sterile plants. To investigate the mechanism underlying this reduction, detailed analysis of the 5' and 3' termini of these transcripts was conducted. Using 3' RACE analysis, the polyadenylation sites of the 1.6- and 2.8-kb transcripts were mapped adjacent to a 3' stem-loop, which may play an important role in stabilizing their 3' ends. No difference was found between the polyadenylation sites in sterile and fertility-restored microspores that could account for the differences in orf355-orf77 transcript levels. The 5' terminus of the 1.6-kb transcript was further studied by primer extension; the result revealed that there was a deletion of nine nucleotides only in fertility-restored microspores, and that this deletion eliminated a 5' stem-loop sequence. We propose that the elimination of the 5' stem-loop in the fertility-restored microspores could be the cause of the degradation of the 1.6-kb transcript. Because the 2.8-kb transcript can be cleaved to generate the 1.6-kb transcript, the amount of the 2.8-kb transcript is also reduced in fertility-restored microspores.