The first A-to-I RNA editome of hemipteran species Coridius chinensis reveals overrepresented recoding and prevalent intron editing in early-diverging insects.

BACKGROUND: Metazoan adenosine-to-inosine (A-to-I) RNA editing resembles A-to-G mutation and increases proteomic diversity in a temporal-spatial manner, allowing organisms adapting to changeable environment. The RNA editomes in many major animal clades remain unexplored, hampering the understanding on the evolution and adaptation of this essential post-transcriptional modification. METHODS: We assembled the chromosome-level genome of Coridius chinensis belonging to Hemiptera, the fifth largest insect order where RNA editing has not been studied yet. We generated ten head RNA-Seq libraries with DNA-Seq from the matched individuals. RESULTS: We identified thousands of high-confidence RNA editing sites in C. chinensis. Overrepresentation of nonsynonymous editing was observed, but conserved recoding across different orders was very rare. Under cold stress, the global editing efficiency was down-regulated and the general transcriptional processes were shut down. Nevertheless, we found an interesting site with "conserved editing but non-conserved recoding" in potassium channel Shab which was significantly up-regulated in cold, serving as a candidate functional site in response to temperature stress. CONCLUSIONS: RNA editing in C. chinensis largely recodes the proteome. The first RNA editome in Hemiptera indicates independent origin of beneficial recoding during insect evolution, which advances our understanding on the evolution, conservation, and adaptation of RNA editing.

New comparative genomic evidence supporting the proteomic diversification role of A-to-I RNA editing in insects.

Adenosine-to-inosine (A-to-I) RNA editing, resembling A-to-G mutation, confers adaptiveness by increasing proteomic diversity in a temporal-spatial manner. This evolutionary theory named "proteomic diversifying hypothesis" has only partially been tested in very few organisms like Drosophila melanogaster, mainly by observing the positive selection on nonsynonymous editing events. To find additional genome-wide evidences supporting this interesting assumption, we retrieved the genomes of four Drosophila species and collected 20 deep-sequenced transcriptomes of different developmental stages and neuron populations of D. melanogaster. We systematically profiled the RNA editomes in these samples and performed meticulous comparative genomic analyses. Further evidences were found to support the diversifying hypothesis. (1) None of the nonsynonymous editing sites in D. melanogaster had ancestral G-alleles, while the silent editing sites had an unignorable fraction of ancestral G-alleles; (2) Only very few nonsynonymous editing sites in D. melanogaster had corresponding G-alleles derived in the genomes of sibling species, and the fraction of such situation was significantly lower than that of silent editing sites; (3) The few nonsynonymous editing with corresponding G-alleles had significantly more variable editing levels (across samples) than other nonsynonymous editing sites in D. melanogaster. The proteomic diversifying nature of RNA editing in Drosophila excludes the restorative role which favors an ancestral G-allele. The few fixed G-alleles in sibling species might facilitate the adaptation to particular environment and the corresponding nonsynonymous editing in D. melanogaster would introduce stronger advantage of flexible proteomic diversification. With multi-Omics data, our study consolidates the nature of evolutionary significance of A-to-I RNA editing sites in model insects.

Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes.

Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent RNA modification in the nervous systems of metazoans. To study the biological significance of RNA editing, we first have to accurately identify these editing events from the transcriptome. The genome-wide identification of RNA editing sites remains a challenging task. In this review, we will first introduce the occurrence, regulation, and importance of A-to-I RNA editing and then describe the established bioinformatic procedures and difficulties in the accurate identification of these sit esespecially in small sized non-model insects. In brief, (1) to obtain an accurate profile of RNA editing sites, a transcriptome coupled with the DNA resequencing of a matched sample is favorable; (2) the single-cell sequencing technique is ready to be applied to RNA editing studies, but there are a few limitations to overcome; (3) during mapping and variant calling steps, various issues, like mapping and base quality, soft-clipping, and the positions of mismatches on reads, should be carefully considered; (4) Sanger sequencing of both RNA and the matched DNA is the best verification of RNA editing sites, but other auxiliary evidence, like the nonsynonymous-to-synonymous ratio or the linkage information, is also helpful for judging the reliability of editing sites. We have systematically reviewed the understanding of the biological significance of RNA editing and summarized the methodology for identifying such editing events. We also raised several promising aspects and challenges in this field. With insightful perspectives on both scientific and technical issues, our review will benefit the researchers in the broader RNA editing community.

Potential reuse of domestic organic residues as soil organic amendment in the current waste management system in Australia, China, and The Netherlands.

Soil organic carbon (SOC) is essential for most soil functions. Changes in land use from natural land to cropland disrupt long-established SOC balances and reduce SOC levels. The intensive use of chemical fertilisers in modern agriculture accelerates the rate of SOC depletion. Domestic organic residues (DOR) are a valuable source of SOC replenishment with high carbon content. However, there is still a lack of knowledge and data regarding whether and to what extent DOR can contribute to replenishing SOC. This paper aims to unpack the potential of DOR as a SOC source. Total SOC demand and annual SOC loss are defined and calculated. The carbon flow within different DOR management systems is investigated in three countries (China, Australia, and The Netherlands). The results show that the total SOC demand is too large to be fulfilled by DOR in a short time. However, DOR still has a high potential as a source of SOC as it can mitigate the annual SOC loss by up to 100%. Achieving this 100% mitigation requires a shift to more circular management of DOR, in particular, more composting, and direct land application instead of landfilling and incineration (Australia and China), or a higher rate of source separation of DOR (The Netherlands). These findings form the basis for future research on DOR recycling as a SOC source.

Monitoring land cover change and its dynamic mechanism on the Qehan Lake Basin, Inner Mongolia, North China, during 1977-2013.

The Qehan Lake Basin is located in the north of the Otindag Sandy Land, where the fragile eco-environment is sensitive to climate change and human activity. We analyzed land cover change and the concomitant processes of ecological change based on multi-spectral scanning (MSS), thematic mapper (TM), and enhanced TM (ETM+) images. The results showed that from 1977 to 2000, the area of dune sand increased significantly by 840.2 km2, while the area of high cover grassland (HCGL), medium cover grassland (MCGL), and low cover grassland (LCGL) reduced by 140.6, 207.3, and 463.3 km2, respectively. Additionally, the area of wetland decreased by 112.9 km2. During the period of 1977 to 2000, the land cover condition index (LCCI) reached a low of 27.7, which indicated serious eco-environmental challenges in the Qehan Lake watershed. However, the process of desertification was reversed, and vegetation cover was gradually restored after 2000. From 2000 to 2013, the area of LCGL increased by 369.2 km2 (13.4%), while the area of dune sand decreased by 560.1 km2 (29.4%). The LCCI improved to reach 29.18 in 2013, demonstrating a significant eco-environmental improvement. Although climate change, human activity, and ecological policies have together determined the scope and extent of desertification in the watershed, the most fundamental factor in the restoration of vegetation was precipitation.

Climatic implications on variations of Qehan Lake in the arid regions of Inner Mongolia during the recent five decades.

The Qehan Lake Basin (QLB) and its system of lakes are located in a marginal monsoon zone and are extremely sensitive to global climate change. In this paper, using aerial photographs from different periods, in addition to MSS, TM, and ETM images, and combining these with regional topographic maps, we analyze lake area changes from 1958 to 2010 and the relation between Qehan Lake (QL) and climate variability. Our results indicate that there was a relatively high lake level in 1959, when the area and volume of the lake were 118.9 km2 and 151.9 × 106 m3, respectively, but this level was subject to a shrinking trend until 2010, when the lake area was only 28.1 km2, and the water volume was 41.1 × 106 m3. West Qehan Lake (WQL) has experienced severe water shrinkage and lake level fluctuation. In 1958, WQL was 80.2 km2 in area and 124.1 × 106 m3 in volume. However, due to a rapid decrease in precipitation and increases in both temperature and evaporation, it began to dry up in 2002. The WQL Water area decreased by 1.82 km2/a, and the lake level declined by 7 m during 1958-2002, so it became an ephemeral lake.

Genome-Wide Identification of PYL/RCAR ABA Receptors and Functional Analysis of LbPYL10 in Heat Tolerance in Goji (Lycium barbarum).

The characterization of the PYL/RCAR ABA receptors in a great deal of plant species has dramatically advanced the study of ABA functions involved in key physiological processes. However, the genes in this family are still unclear in Lycium (Goji) plants, one of the well-known economically, medicinally, and ecologically valuable fruit crops. In the present work, 12 homologs of Arabidopsis PYL/RCAR ABA receptors were first identified and characterized from Lycium (L.) barbarum (LbPYLs). The quantitative real-time PCR (qRT-PCR) analysis showed that these genes had clear tissue-specific expression patterns, and most of them were transcribed in the root with the largest amount. Among the three subfamilies, while the Group I and Group III members were down-regulated by extraneous ABA, the Group II members were up-regulated. At 42 °C, most transcripts showed a rapid and violent up-regulation response to higher temperature, especially members of Group II. One of the genes in the Group II members, LbPYL10, was further functionally validated by virus-induced gene silencing (VIGS) technology. LbPYL10 positively regulates heat stress tolerance in L. barbarum by alleviating chlorophyll degradation, thus maintaining chlorophyll stability. Integrating the endogenous ABA level increase following heat stress, it may be concluded that LbPYL-mediated ABA signaling plays a vital role in the thermotolerance of L. barbarum plants. Our results highlight the strong potential of LbPYL genes in breeding genetically modified L. barbarum crops that acclimate to climate change.

Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites.

Adenosine-to-inosine (A-to-I) RNA editing recodes the genome and confers flexibility for the organisms to adapt to the environment. It is believed that RNA recoding sites are well suited for facilitating adaptive evolution by increasing the proteomic diversity in a temporal-spatial manner. The function and essentiality of a few conserved recoding sites are recognized. However, the experimentally discovered functional sites only make up a small corner of the total sites, and there is still the need to expand the repertoire of such functional sites with bioinformatic approaches. In this study, we define a new category of RNA editing sites termed 'conserved editing with non-conserved recoding' and systematically identify such sites in Drosophila editomes, figuring out their selection pressure and signals of adaptation at inter-species and intra-species levels. Surprisingly, conserved editing sites with non-conserved recoding are not suppressed and are even slightly overrepresented in Drosophila. DNA mutations leading to such cases are also favoured during evolution, suggesting that the function of those recoding events in different species might be diverged, specialized, and maintained. Finally, structural prediction suggests that such recoding in potassium channel Shab might increase ion permeability and compensate the effect of low temperature. In conclusion, conserved editing with non-conserved recoding might be functional as well. Our study provides novel aspects in considering the adaptive evolution of RNA editing sites and meanwhile expands the candidates of functional recoding sites for future validation.

Integrated life cycle assessment of biotreatment and agricultural use of domestic organic residues: Environmental benefits, trade-offs, and impacts on soil application.

Extensive agricultural activities have been shown to degrade soils, promoting research into improving soil quality. One such method is to increase the amount of organic matter in the soil, and domestic organic residues (DOR) are commonly used for this purpose. The environmental impact of DOR-derived products, from production to agricultural application, remains unclear in current research. With the aim to have a more comprehensive understanding of the challenges and opportunities in DOR management and reuse, this study extended the boundaries of Life Cycle Assessment (LCA) to include the transport, treatment, and application of treated DOR on a national level while also quantifying soil carbon sequestration that has been less addressed in relevant LCA studies. This study focuses on The Netherlands, where incineration predominates, as a representative case to explore the benefits and trade-offs of moving towards more biotreatment for DOR. Two main biotreatments were considered, composting and anaerobic digestion. The results indicate that biotreatment of kitchen and yard residues generally has higher environmental impacts than incineration, including increased global warming and fine particulate matter formation. However, biotreatment of sewage sludge has lower environmental impacts than incineration. Substitution of nitrogen and phosphorus fertilisers with compost reduces mineral and fossil resource scarcity. In fossil-based energy systems like The Netherlands, replacing incineration with anaerobic digestion yields the highest benefit for fossil resource scarcity (61.93 %) due to energy recovery from biogas and the predominant use of fossil resources in the Dutch energy system. These findings indicate that replacing incineration with biotreatment of DOR may not benefit all impact categories in LCA. The environmental performance of substituted products can significantly influence the environmental benefits of increased biotreatment. Future studies or implementation of increased biotreatment should consider trade-offs and local context.

IRP30 promotes worker egg-laying in bumblebee, Bombus terrestris (Hymenoptera: Apidae).

Bumblebees are important pollinators that have evolved between solitary and advanced eusocial insects. Compared with advanced honeybees, workers of social bumblebee species are prone to laying eggs during the competition phase, which leads to the end of the colony. Therefore, worker reproductive behavior has become a popular research topic for exploring various biological phenomena. Here, we demonstrate a novel reproduction-related function of an immune response protein-encoding gene (Immune Responsive Protein 30, IRP30) in Bombus terrestris by employing RNA interference (RNAi) and a transgenic Drosophila melanogaster system. The results show that worker egg-laying was significantly affected by IRP30 expression levels (P < 0.01). Compared with those in the dsGFP-treated groups, the first egg-laying time was delayed by 3.7 d and the egg number was decreased by 41% in the dsIRP30-treated group. In addition, the average size of the largest oocyte and the relative mRNA expression levels of Vg (vitellogenin) were significantly reduced in the dsIRP30-treated group (P < 0.05). Cellular localization by immunofluorescence demonstrated that IRP30 has important functions in the germ cells of workers' ovarioles. Overexpression of IRP30 was confirmed to increase the reproductive capability of the transgenic D. melanogaster. In conclusion, IRP30 regulates worker egg-laying by affecting the expression of Vg, the size of the ovary and the formation of the oocyte. These findings provide essential information for understanding the mechanisms underlying worker reproductive regulation.

Long non-coding RNA NEAT1 mediates MPTP/MPP+-induced apoptosis via regulating the miR-124/KLF4 axis in Parkinson's disease.

Accumulating evidence suggests that dysregulation of long non-coding RNAs is closely associated with various human diseases, including Parkinson's disease (PD). However, the role of nuclear-enriched abundant transcript 1 (NEAT1) in the PD process remains unclear. The number of TH+ cells was reduced, and the expression levels of NEAT1 and Krüppel-like factor 4 (KLF4) were increased in the midbrain of MPTP-HCl-treated mice. In addition, the expression of cleaved-caspase-3 (cleaved-casp-3) and Bax (apoptosis-related proteins) was increased, while the expression of Bcl-2 (anti-apoptotic protein) was reduced in MPTP-HCl-treated mice. The expression levels of NEAT1 and KLF4 were increased in MPP+-treated SH-SY5Y cells. Knockdown of NEAT1 promoted cell viability and decreased apoptosis in MPP+-treated SH-SY5Y cells, which could be reversed by upregulating KLF4. KLF4 was verified as a direct target of miR-124, and miR-124 could particularly bind to NEAT1. Downregulation of NEAT1 significantly increased cell viability and decreased apoptosis by regulating miR-124 expression in MPP+-treated SH-SY5Y cells. Additionally, interference of NEAT1 increased the number of TH+ cells and miR-124 expression, while reduced apoptosis and expression of KLF4 in vivo. NEAT1 knockdown increased cell viability and suppressed apoptosis in PD via regulating the miR-124/KLF4 axis, providing a promising avenue for the treatment of PD.