Development of the transcriptome for a sediment ecotoxicological model species, Chironomus dilutus

tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis

A class of noncoding RNAs, referred to as tsRNAs, is emerging with a potential to exert a new layer in gene regulation. These RNAs are breakdown products of tRNAs, either through active processing or passive cleavage or both. Since tRNAs are part of the general machinery for translation, their expression levels and activities are tightly controlled, raising the possibility that their breakdown products, tsRNAs, may provide a link between the overall translational status of a cell to specific changes in gene regulatory network. We hypothesize that Drosophila pupation, being a special developmental stage during which there is a global limitation of nutrients, represents a system in which such a link may readily reveal itself. We show that specific tsRNAs indeed show a dynamic accumulation upon entering the pupal stage. We describe experiments to characterize the mode of tsRNA action and, through the use of such gained knowledge, conduct a genome-wide analysis to assess the functions of dynamically expressed tsRNAs. Our results show that the predicted target genes are highly enriched in biological processes specific to this stage of development including metamorphosis. We further show that tsRNA action is required for successful pupation, providing direct support to the hypothesis that tsRNAs accumulated during this stage are critical to the gene expression program at this stage of development.

Marine Biomass-Supported Nano Zero-Valent Iron for Cr(VI) Removal: A Response Surface Methodology Study

Heavy metal ions such as Cr(VI) pose great hazards to the environment, which requests materials and methods for decontamination. Nano zero-valent iron (nZVI) has emerged as a promising candidate for Cr(VI) removal. Herein, harnessing the merits of marine biomass, a heterogeneous water treatment system for the decontamination of Cr(VI) is developed based on the in situ immobilization of nZVI on the seashell powder (SP)-derived porous support. A response surface methodology (RSM) study involving three independent factors is designed and conducted to direct material synthesis and reaction design for products with optimal performances. Under optimal synthetic conditions, the nZVI-loaded seashell powder (SP@nZVI), which is characterized in detail by scanning electron microscope (SEM), X-ray diffraction (XRD), and Fourier-transform infrared spectroscopy (FTIR), results in a 79% increase in the removal efficiency of Cr(VI) compared to free nZVI. Mechanism studies show that the removal of Cr(VI) by SP@nZVI conforms to the Langmuir adsorption model with a quasi-second order kinetic equation, in which redox reactions between nZVI and Cr(VI) occurred at the SP surface. The results of this work are expected to benefit the reuse of bioresource waste in developing environmental remediation materials.

Identification of toxicity factors and causal analysis of toxicity in surface sediments from Liaohe river basin, Northeast China using an effect guidance strategy

Sediments play a pivotal role in maintaining the aquatic ecological status of rivers. However, the determination of the key toxicants that consider the combined effects of all sediment-related contaminants are still challenging and necessary for an appropriate sediment risk assessment. The effects of sediments on aquatic organisms have been reported in Liaohe River, but their key toxicity factors are not well known. To determine the key toxicity factors, twenty-six surface sediment samples from Liaohe River tributaries in Northeast China were collected. Acute toxicity test of midge larvae results showed that 6 of 26 tributaries had obvious toxic effects, with survival rates of 37%-57% (p < 0.05). The masking test showed that the main pollutants in the surface sediments of T7 and T16 were metals, that of T8 was an organic pollutant, those of T19 and T26 were organic pollutants and ammonia, and those of T17 were heavy metal and ammonia. Chemical analysis showed that the relatively high concentrations of ammonia were only presented in surface sediments of T17, T19, and T26, with PTU of 1.5, 1.2 and 1.1, respectively, whereas heavy metals were markedly high in surface sediments from T7 and T16, with PTU of 0.92 and 0.61, respectively. Interestingly, the observed toxicity in surface sediments agreed with the toxicity predicted by chemical analysis Moreover, the significant correlation between the survival and volume ratio of the sediment and overlying water confirmed ammonia nitrogen was key toxicity factor in T17, T19, and T26, whereas Cu was the key toxicity factor in T7 that cause the biological toxicity. In conclusion, the major toxic factors of ammonia and copper in the sediments were identified. Moreover, our study suggested that effect guidance strategy was an effective method for sediment quality assessment.

First transcriptome of the copepod Gladioferens pectinatus subjected to chronic contaminant exposures

Contaminants are often at low concentrations in ecosystems and their effects on exposed organisms can occur over long periods of time and across multiple generations. Alterations to subcellular mechanistic pathways in response to exposure to contaminants can provide insights into mechanisms of toxicity that methods measuring higher levels of biological may miss. Analysis of the whole transcriptome can identify novel mechanisms of action leading to impacts in exposed biota. The aim of this study was to characterise how exposures to copper, benzophenone and diclofenac across multiple generations altered molecular expression pathways in the marine copepod Gladioferens pectinatus. Results of the study demonstrated differential gene expression was observed in cultures exposure to diclofenac (569), copper (449) and benzophenone (59). Pathways linked to stress, growth, cellular and metabolic processes were altered by exposure to all three contaminants with genes associated with oxidative stress and xenobiotic regulation also impacted. Protein kinase functioning, cytochrome P450, transcription, skeletal muscle contraction/relaxation, mitochondrial phosphate translocator, protein synthesis and mitochondrial methylation were all differentially expressed with all three chemicals. The results of the study also suggested that using dimethyl sulfoxide as a dispersant influenced the transcriptome and future research may want to investigate it's use in molecular studies. Data generated in this study provides a first look at transcriptomic response of G. pectinatus exposed to contaminants across multiple generations, future research is needed to validate the identified biomarkers and link these results to apical responses such as population growth to demonstrate the predictive capacity of molecular tools.

Construction and analysis of the protein-protein interaction network for the detoxification enzymes of the silkworm, Bombyx mori

Detoxification enzymes are necessary for insects to metabolize toxic substances and maintain physiological activities. Cytochromes P450 (CYPs), glutathione S-transferases (GSTs), and carboxylesterase (CarEs) are the main detoxification enzymes in insects. In addition, UDP-glucosyltransferase and ATP-binding cassette transporter also participate in the process of material metabolism. This study collected proteins related to detoxification in the silkworm, Bombyx mori (Lepidoptera: Bombycidae). And we performed Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis on these proteins to understand their biological function. We constructed the protein-protein interaction network for the silkworm's detoxification enzymes and analyzed the network's topological properties. We found that BGIBMGA014046-TA, BGIBMGA003221-TA, BGIBMGA011092-TA, BGIBMGA000074-TA, and LOC732976 are the essential proteins in the network. These proteins are primarily involved in the process of ribosome biogenesis and may be related to protein synthesis. We integrated GO, KEGG, and network analysis and found that ribosome-associated protein and GSTs played a vital role in the detoxification process.

Multi-generational exposure to fipronil, 2,4-D, and their mixtures in Chironomus sancticaroli: Biochemical, individual, and population endpoints

Conventional farming delivers a range of pesticides to aquatic ecosystems leading to implications for the indigenous species. Due to the multiple applications and persistence of molecules, organisms may be exposed for a prolonged period over multiple generations. The present study outlines a full life-cycle design over three generations of Chironomus sancticaroli exposed to the insecticide fipronil, the herbicide 2,4-D, and their mixtures. The experiment started with newly hatched larvae from the parental generation and lasted with the emerged adults from the second generation. Five nominal concentrations of fipronil and 2,4-D were tested, as well as six combinations of both pesticides. As additional responses, the total carbohydrates and the lipid classes were evaluated in the parental generation. The first and second generations were more susceptible to the tested compounds compared with the parental ones. Survival of larvae and pupae was decreased by both pesticides and their mixtures along with the generations. Only fipronil impaired the survival of emerged adults. Both pesticides (isolated and in the mixture) altered the emergence and the fraction of males and females. Moreover, the number of eggs produced, and their hatchability decreased. Only one combination of the pesticides increased the content of carbohydrates. Fipronil, 2,4-D, and its mixture altered the profile of the lipid classes. All mixture treatments and the three highest concentrations of fipronil extinguished the population of C. sancticaroli at the end of the first generation. In the remaining treatments with the insecticide, the population did not survive the second generation. Only three concentrations of 2,4-D and the control persisted until the end of the experiment. The results indicate that a prolonged exposition to these pesticides may disrupt the natural populations of exposed organisms with consequences to ecosystems' functioning, considering the importance of chironomids to aquatic and terrestrial environments.

Persistent pesticides: effects of endosulfan at the molecular level on the aquatic invertebrate Chironomus riparius

Although banned in multiple areas, due to its persistence in the environment, endosulfan constitutes a significant environmental concern. In this work, fourth instar Chironomus riparius larvae were exposed at environmentally relevant endosulfan concentrations of 0.1, 1, and 10 μg/L for 24 h to analyze the possible effects of this acaricide on gene expression and enzymatic activity. Transcriptional changes were studied through the implementation of a real-time polymerase chain reaction array with 42 genes related to several metabolic pathways (endocrine system, detoxification response, stress response, DNA reparation, and immune system). Moreover, glutathione-S-transferase (GST), phenoloxidase (PO), and acetylcholinesterase (AChE) activities were assessed. The five pathways were differentially altered by endosulfan exposure with significant changes in the E93, Dis, MAPR, Met, InR, GSTd3, GSTt3, MRP1, hsp70, hsp40, hsp24, ATM, PARP, Proph, and Def genes. Besides, all of the measured enzymatic activities were modified, with increased activity of GST, followed by PO and AChE. In summary, the results reflected the effects provoked in C. riparius at molecular level despite the absence of lethality. These data raise concerns about the strong alteration on different metabolic routes despite the low concentrations used. Therefore, new risk assessment strategies should consider include the effects at the sub-organismal level as endpoints in addition to the classical ecologically relevant parameters (such as survival). This endeavor will facilitate a comprehensive evaluation of toxicants in the environment.

A deep insight into the transcriptome of midgut and fat body reveals the toxic mechanism of fluoride exposure in silkworm

Fluoride generally exists in the natural environment, and has been reported to induce serious environmental hazard to animals, plants, and even humans via ecological cycle. Silkworm, Bombyx mori, which showed significant growth and reproductivity reduction when exposed to fluoride, has become a model to evaluate the toxicity of fluoride. However, the detailed mechanism underlying fluoride toxicity and corresponding transport proteins remain unclear. In this study, we performed RNA-seq of the larval midgut and fat body with fluoride exposure and normal treatment. Differential analysis showed that there were 4405 differentially expressed genes in fat body and 4430 DEGs in midgut with fluoride stress. By Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, we identified several key pathways involved in the fluoride exposure and poisoning. We focused on the oxidative phosphorylation and MAPK signal pathway. QRT-PCR confirmed that oxidative phosphorylation process was remarkably inhibited by fluoride exposure and resulted in the blocking of ATP synthesis. The MAPK signal pathway was stimulated via phosphorylation signal transduction. Moreover, by protein structure analysis combined with the DEGs, we screen 36 potential membrane proteins which might take part in transporting fluoride. Taken together, the results of our study expanded the underlying mechanisms of fluoride poisoning on silkworm larval growth and development, and implied potential fluoride transport proteins in silkworm.

Multi-Level Gene Expression in Response to Environmental Stress in Aquatic Invertebrate Chironomids: Potential Applications in Water Quality Monitoring

In freshwater ecosystems, aquatic invertebrates are influenced continuously by both physical stress and xenobiotics. Chironomids (Diptera; Chironomidae), or non-biting midges, are the most diverse and abundant invertebrates in freshwater habitats. They are a fundamental link in food chains of aquatic ecosystems. Chironomid larvae tolerate stress factors in their environments via various physiological processes. At the molecular level, environmental pollutants induce multi-level gene responses in Chironomus that regulate cellular protection through the activation of defense processes. This paper reviews literature on the transcriptional responses of biomarker genes to environmental stress in chironomids at the molecular level, in studies conducted from 1991 to 2020 (120 selected literatures of 374 results with the keywords "Chironomus and gene expression" by PubMed search tool). According to these studies, transcriptional responses in chironomids vary depending on the type of stress factor and defensive responses associated with antioxidant activity, the endocrine system, detoxification, homeostasis and stress response, energy metabolism, ribosomal machinery, apoptosis, DNA repair, and epigenetics. These data could provide a comprehensive overview of how Chironomus species respond to pollutants in aquatic environments. Furthermore, the transcriptomic data could facilitate the development of genetic tools for water quality and environmental monitoring based on resident chironomid species.

Transcriptomic analysis reveals common pathways and biomarkers associated with oxidative damage caused by mitochondrial toxicants in Chironomus dilutus

A variety of chemicals are capable of provoking mitochondrial dysfunction and thereby contribute to metabolic disorder related effects in wildlife and human. For better identifying new mitochondrial toxicants and assessing mitochondria-related risk, an in-depth understanding of toxic mechanisms and biomarkers should be attained. In the current study, a representative mitotoxicant, azoxystrobin, was assessed for lethal and sublethal outcomes in Chironomus dilutus after 96-h exposure and the toxic mechanism was explored. Global transcriptomic profiles by RNA-sequencing revealed that ampk, acc1, atp2a, gsk3b, pi3k, fak, atr, chk1, and map3k5 were the key genes which involved in the toxic action of azoxystrobin and could serve as potential molecular biomarkers. A major network of common toxicity pathways was then developed for mitotoxicants towards aquatic insects. In particular, calcium ion-PI3K/AKT and cAMP-AMPK-lethality pathways were demonstrated, in addition to the well-known mitochondrial electron transfer-oxidative damage-apoptosis pathway. These analyses could help developing adverse outcome pathways that integrate toxicological information at various levels and support more effective risk assessment and management of mitotoxicants.