Structural basis of chorismate isomerization by Arabidopsis ISOCHORISMATE SYNTHASE1.

Salicylic acid (SA) plays a crucial role in plant defense against biotrophic and semi-biotrophic pathogens. In Arabidopsis (Arabidopsis thaliana), isochorismate synthase 1 (AtICS1) is a key enzyme for the pathogen-induced biosynthesis of SA via catalytic conversion of chorismate into isochorismate, an essential precursor for SA synthesis. Despite the extensive knowledge of ICS1-related menaquinone, siderophore, tryptophan (MST) enzymes in bacteria, the structural mechanisms for substrate binding and catalysis in plant isochorismate synthase (ICS) enzymes are unknown. This study reveals that plant ICS enzymes catalyze the isomerization of chorismate through a magnesium-dependent mechanism, with AtICS1 exhibiting the most substantial catalytic activity. Additionally, we present high-resolution crystal structures of apo AtICS1 and its complex with chorismate, offering detailed insights into the mechanisms of substrate recognition and catalysis. Importantly, our investigation indicates the existence of a potential substrate entrance channel and a gating mechanism regulating substrate into the catalytic site. Structural comparisons of AtICS1 with MST enzymes suggest a shared structural framework with conserved gating and catalytic mechanisms. This work provides valuable insights into the structural and regulatory mechanisms governing substrate delivery and catalysis in AtICS1, as well as other plant ICS enzymes.

A chromosome-level genome assembly of yellow stem borer (Scirpophaga incertulas).

The yellow stem borer Scirpophaga incertulas is the dominant pest of rice in tropical Asia. However, the lack of genomic resources makes it difficult to understand their invasiveness and ecological adaptation. A high-quality chromosome-level genome of S. incertulas, a monophagous rice pest, was assembled by combining Illumina short reads, PacBio HiFi long sequencing, and Hi-C scaffolding technology. The final genome size was 695.65 Mb, with a scaffold N50 of 28.02 Mb, and 93.50% of the assembled sequences were anchored to 22 chromosomes. BUSCO analysis demonstrated that this genome assembly had a high level of completeness, with 97.65% gene coverage. A total of 14,850 protein-coding genes and 366.98 Mb of transposable elements were identified. In addition, comparative genomic analyses indicated that chemosensory processes and detoxification capacity may play critical roles in the specialized host preference of S. incertulas. In summary, the chromosome-level genome assembly of S. incertulas provides a valuable genetic resource for understanding the biological characteristics of its invasiveness and developing an efficient management strategy.

The elucidation of the anti-inflammatory mechanism of EMO in rheumatoid arthritis through an integrative approach combining bioinformatics and experimental verification.

Introduction: Emodin (EMO), a natural derivative of the anthraquinone family mainly extracted from rhubarb (Rheum palmatum), has previously been demonstrated to possess superior anti-inflammatory properties from a single target or pathway. In order to explore the underlying mechanism of action of EMO against rheumatoid arthritis (RA), a network pharmacology approach was employed. Methods: A gene expression profile from GSE55457 available from the Gene Expression Omnibus (GEO) database was used to identify the targets of EMO action. Further, single cell RNA sequencing data from GEO database of RA patients (GSE159117) were downloaded and analysed. To further investigate the anti-RA effect of EMO on MH7A cells, the expression of IL-6 and IL-1ß were monitored. Finally, RNA-seq analyses were conducted on synovial fibroblasts from EMO-treated. Result: We screened the key targets of EMO against RA using network pharmacology methods, including HMGB1, STAT1, EGR1, NR3C1, EGFR, MAPK14, CASP3, CASP1, IL4, IL13, IKBKB and FN1, and their reliability was verified using ROC curve. Single-cell RNA sequencing data analysis showed that these core target proteins mainly played a role by modulating monocytes. The anti-RA effect of EMO was further verified with MH7A cells, which showed that EMO could block cell differentiation and reduce the expression of IL-6 and IL-1ß. WB experiments confirmed that EMO could affect the expression of COX2, HMBG1 and the phosphorylation of p38. Finally, sequencing of synovial fibroblasts from rats treated with EMO showed consistent results with those predicted and verified, further proving the anti-inflammatory effect of EMO. Conclusion: Our research shows that EMO inhibits inflammatory response of rheumatoid arthritis (RA) by targeting HMGB1, STAT1, EGR1, NR3C1, EGFR, MAPK14, CASP3, CASP1, IL4, IL13, IKBKB, FN1 and Monocytes/macrophages.

Integrating Network Pharmacology and Experimental Validation to Explore the Pharmacological Mechanism of Astragaloside IV in Treating Bleomycin-Induced Pulmonary Fibrosis.

Purpose: Our study aims to reveal the pharmacological mechanism of Astragaloside IV in the treatment of pulmonary fibrosis(PF) through network pharmacology and experimental validation. Methods: We first determined the in vivo anti-pulmonary fibrosis effect of Astragaloside IV by HE, MASSON staining, and lung coefficients, then used network pharmacology to predict the signaling pathways and molecularly docked key pathway proteins, and finally validated the results by in vivo and in vitro experiments. Results: In in vivo experiments, we found that Astragaloside IV improved body weight (P < 0.05), increased lung coefficients (P < 0.05), and reduced lung inflammation and collagen deposition in mice with pulmonary fibrosis. The network pharmacology results showed that Astragaloside IV had 104 cross-targets with idiopathic pulmonary fibrosis, and the results of KEGG enrichment analysis indicated that cellular senescence could be an important pathway for Astragaloside IV in the treatment of pulmonary fibrosis. Astragaloside IV also bound well to senescence-associated proteins, according to molecular docking results. The results of both in vivo and in vitro experiments showed that Astragaloside IV significantly inhibited senescence protein markers such as P53, P21, and P16 and delayed cellular senescence (P < 0.05). In in vivo experiments, we also found that Astragaloside IV reduced the production of SASPs (P < 0.05), and in in vitro experiments, Astragaloside IV also reduced the production of ROS. In addition, by detecting epithelial-mesenchymal transition(EMT)-related marker protein expression, we also found that Astragaloside IV significantly inhibited the development of EMT in both in vivo and in vitro experiments (P < 0.05). Conclusion: Our research found that Astragaloside IV could alleviate bleomycin-induced PF by preventing cellular senescence and EMT.

High circadian stimulus lighting therapy for depression: Meta-analysis of clinical trials.

Although bright light therapy (BLT) has been widely used in the clinical treatment of depression, the antidepressant effect of BLT is not well understood. Considering the connection between depression and disrupted circadian rhythm, we assumed the model of human circadian phototransduction could be more accurate in evaluating the efficacy of BLT for depression compared to light level and spectrum. A systematic review and meta-analysis were conducted and the CS (circadian stimulus) model was used to quantify the efficacy of lighting in BLT. Articles published up to June 2022 were searched in COCHRANE, EMBASE, MEDLINE, and Web of Science. Randomized clinical trials included articles using high circadian stimulus (H-CS, CS > 0.1) as lighting therapy for people with depressive disorder vs. a control group (CS < 0.1). The treatment effect was estimated by calculating the mean difference (MD) with 95% confidence intervals (CIs). Seven trials involving 258 participants met the inclusion criteria. In this sample size, H-CS lighting was associated with a significant reduction in depressive symptoms (MD = -5.56, 95% CI = -9.22 to -1.90, P = 0.003, I 2 = 64%). According to the meta-analysis, CS can be employed for the clinical evaluation of BLT for patients with depressive disorder and exposure to H-CS lighting significantly reduced depressive symptoms among adults. A range of CS > 0.57 was obtained, during which different lighting parameter combinations (e.g., light levels, spectra, duration, and light distribution) could achieve better treatment for depression. Systematic review registration: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021253648.

Parasite reliance on its host gut microbiota for nutrition and survival.

Studying the microbial symbionts of eukaryotic hosts has revealed a range of interactions that benefit host biology. Most eukaryotes are also infected by parasites that adversely affect host biology for their own benefit. However, it is largely unclear whether the ability of parasites to develop in hosts also depends on host-associated symbionts, e.g., the gut microbiota. Here, we studied the parasitic wasp Leptopilina boulardi (Lb) and its host Drosophila melanogaster. Results showed that Lb successfully develops in conventional hosts (CN) with a gut microbiota but fails to develop in axenic hosts (AX) without a gut microbiota. We determined that developing Lb larvae consume fat body cells that store lipids. We also determined that much larger amounts of lipid accumulate in fat body cells of parasitized CN hosts than parasitized AX hosts. CN hosts parasitized by Lb exhibited large increases in the abundance of the bacterium Acetobacter pomorum in the gut, but did not affect the abundance of Lactobacillus fructivorans which is another common member of the host gut microbiota. However, AX hosts inoculated with A. pomorum and/or L. fructivorans did not rescue development of Lb. In contrast, AX larvae inoculated with A. pomorum plus other identified gut community members including a Bacillus sp. substantially rescued Lb development. Rescue was further associated with increased lipid accumulation in host fat body cells. Insulin-like peptides increased in brain neurosecretory cells of parasitized CN larvae. Lipid accumulation in the fat body of CN hosts was further associated with reduced Bmm lipase activity mediated by insulin/insulin-like growth factor signaling (IIS). Altogether, our results identify a previously unknown role for the gut microbiota in defining host permissiveness for a parasite. Our findings also identify a new paradigm for parasite manipulation of host metabolism that depends on insulin signaling and the gut microbiota.

Search performance and octopamine neuronal signaling mediate parasitoid induced changes in Drosophila oviposition behavior.

Making the appropriate responses to predation risk is essential for the survival of an organism; however, the underlying mechanisms are still largely unknown. Here, we find that Drosophila has evolved an adaptive strategy to manage the threat from its parasitoid wasp by manipulating the oviposition behavior. Through perception of the differences in host search performance of wasps, Drosophila is able to recognize younger wasps as a higher level of threat and consequently depress the oviposition. We further show that this antiparasitoid behavior is mediated by the regulation of the expression of Tdc2 and Tßh in the ventral nerve cord via LC4 visual projection neurons, which in turn leads to the dramatic reduction in octopamine and the resulting dysfunction of mature follicle trimming and rupture. Our study uncovers a detailed mechanism underlying the defensive behavior in insects that may advance our understanding of predator avoidance in animals.

The Dual Functions of a Bracovirus C-Type Lectin in Caterpillar Immune Response Manipulation.

Parasitoids are widespread in natural ecosystems and normally equipped with diverse viral factors to defeat host immune responses. On the other hand, parasitoids can enhance the antibacterial abilities and improve the hypoimmunity traits of parasitized hosts that may encounter pathogenic infections. These adaptive strategies guarantee the survival of parasitoid offspring, yet their underlying mechanisms are poorly understood. Here, we focused on Cotesia vestalis, an endoparasitoid of the diamondback moth Plutella xylostella, and found that C. vestalis parasitization decreases the number of host hemocytes, leading to disruption of the encapsulation reaction. We further found that one bracovirus C-type lectin gene, CvBV_28-1, is highly expressed in the hemocytes of parasitized hosts and participates in suppressing the proliferation rate of host hemocytes, which in turn reduces their population and represses the process of encapsulation. Moreover, CvBV_28-1 presents a classical bacterial clearance ability via the agglutination response in a Ca2+-dependent manner in response to gram-positive bacteria. Our study provides insights into the innovative strategy of a parasitoid-derived viral gene that has dual functions to manipulate host immunity for a successful parasitism.

Neofunctionalization of an ancient domain allows parasites to avoid intraspecific competition by manipulating host behaviour.

Intraspecific competition is a major force in mediating population dynamics, fuelling adaptation, and potentially leading to evolutionary diversification. Among the evolutionary arms races between parasites, one of the most fundamental and intriguing behavioural adaptations and counter-adaptations are superparasitism and superparasitism avoidance. However, the underlying mechanisms and ecological contexts of these phenomena remain underexplored. Here, we apply the Drosophila parasite Leptopilina boulardi as a study system and find that this solitary endoparasitic wasp provokes a host escape response for superparasitism avoidance. We combine multi-omics and in vivo functional studies to characterize a small set of RhoGAP domain-containing genes that mediate the parasite's manipulation of host escape behaviour by inducing reactive oxygen species in the host central nervous system. We further uncover an evolutionary scenario in which neofunctionalization and specialization gave rise to the novel role of RhoGAP domain in avoiding superparasitism, with an ancestral origin prior to the divergence between Leptopilina specialist and generalist species. Our study suggests that superparasitism avoidance is adaptive for a parasite and adds to our understanding of how the molecular manipulation of host behaviour has evolved in this system.

Comparative transcriptome analysis reveals a potential mechanism for host nutritional manipulation after parasitization by Leptopilina boulardi.

Parasitoids have been extensively found to manipulate nutrient amounts of their hosts to benefit their own development and survival, but the underlying mechanisms are largely unknown. Leptopilina boulardi (Hymenoptera: Figitidae) is a larval-pupal endoparasitoid wasp of Drosophila melanogaster whose survival relies on the nutrients provided by its Drosophila host. Here, we used RNA-seq to compare the gene expression levels of the host midgut at 24 h and 48 h post L. boulardi parasitization. We obtained 95 and 191 differentially expressed genes (DEGs) in the parasitized host midgut at 24 h and 48 h post L. boulardi parasitization, respectively. A KEGG analysis revealed that several metabolic pathways were significantly enriched in the upregulated DEGs, and these pathways included "starch and sucrose metabolism" and "galactose metabolism". A functional annotation analysis showed that four classes of genes involved in carbohydrate digestion process had increased expression levels in the midgut post L.boulardi parasitization than nonparasitized groups: glucosidase, mannosidase, chitinase and amylase. Genes involved in protein digestion process were also found among the DEGs, and most of these genes, which belonged to the metallopeptidase and serine-type endopeptidase families, were found at higher expression levels in the parasitized host midgut comparing with nonparasitized hosts. Moreover, some immune genes, particularly those involved in the Toll and Imd pathways, also exhibited high expression levels after L.boulardi parasitization. Our study provides large-scale transcriptome data and identifies sets of DEGs between parasitized and nonparasitized host midgut tissues at 24 h and 48 h post L. boulardi parasitization. These resources help improve our understanding of how parasitoid infection affects the nutrient components in the hosts.

Symbiotic bracovirus of a parasite manipulates host lipid metabolism via tachykinin signaling.

Parasites alter host energy homeostasis for their own development, but the mechanisms underlying this phenomenon remain largely unknown. Here, we show that Cotesia vestalis, an endoparasitic wasp of Plutella xylostella larvae, stimulates a reduction of host lipid levels. This process requires excess secretion of P. xylostella tachykinin (PxTK) peptides from enteroendocrine cells (EEs) in the midgut of the parasitized host larvae. We found that parasitization upregulates PxTK signaling to suppress lipogenesis in midgut enterocytes (ECs) in a non-cell-autonomous manner, and the reduced host lipid level benefits the development of wasp offspring and their subsequent parasitic ability. We further found that a C. vestalis bracovirus (CvBV) gene, CvBV 9-2, is responsible for PxTK induction, which in turn reduces the systemic lipid level of the host. Taken together, these findings illustrate a novel mechanism for parasite manipulation of host energy homeostasis by a symbiotic bracovirus gene to promote the development and increase the parasitic efficiency of an agriculturally important wasp species.

Two novel venom proteins underlie divergent parasitic strategies between a generalist and a specialist parasite.

Parasitoids are ubiquitous in natural ecosystems. Parasitic strategies are highly diverse among parasitoid species, yet their underlying genetic bases are poorly understood. Here, we focus on the divergent adaptation of a specialist and a generalist drosophilid parasitoids. We find that a novel protein (Lar) enables active immune suppression by lysing the host lymph glands, eventually leading to successful parasitism by the generalist. Meanwhile, another novel protein (Warm) contributes to a passive strategy by attaching the laid eggs to the gut and other organs of the host, leading to incomplete encapsulation and helping the specialist escape the host immune response. We find that these diverse parasitic strategies both originated from lateral gene transfer, followed with duplication and specialization, and that they might contribute to the shift in host ranges between parasitoids. Our results increase our understanding of how novel gene functions originate and how they contribute to host adaptation.

The complete mitochondrial genome of Leptopilina syphax (Hymenoptera: Figitidae).

Leptopilina syphax (Hymenoptera: Figitidae) is a newly recorded species of parasitic wasp, and it attacks the larval stage of Drosophilidae, mainly the Drosophila species. Few works have been done in the basic study of L. syphax, including the data of mitochondrial genome. In this study, the complete mitochondrial genome of L. syphax (GeneBank accession number: MT649407) was sequenced using Illumina HiSeq X Ten system. The mitochondrial genome is 15,882bp long and comprises 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. Meanwhile, 26 genes are in majority strand, and the remaining 11 genes are in minority strand. The overall base composition is 41.7% for A, 6.0% for G, 13.6% for C, and 38.7% for T, with an A + T content of 80.4%, respectively. We also performed a phylogenetic analysis with other known mitochondrial genomes of some parasitic wasps. The results show that L. syphax is closely related to L. boulardi, which is another Drosophila parasitoid.

Expression and functional characterization of odorant-binding protein genes in the endoparasitic wasp Cotesia vestalis.

Odorant-binding proteins (OBPs) are crucial in insect's olfactory perception, which participate in the initial step of odorant molecules transporting from the external environment to olfactory receptor neurons. To better understand the roles for OBPs in olfactory perception in Cotesia vestalis, a solitary larval endoparasitoid of diamondback moth, Plutella xylostella, we have comprehensively screened the genome of C. vestalis, and obtained 20 CvesOBPs, including 18 classic OBPs and two minus-C OBPs. Motif-pattern analysis indicates that the motifs of C. vestalis OBPs are highly conserved in Hymenoptera. The results of tissue expression analysis show that five OBPs (CvesOBP1/11/12/14/16) are highly expressed in male antennae, whereas six other OBP genes (CvesOBP7/8/13/17/18/19) are significantly transcriptionally enriched in female antennae. The results of RNA interference experiments for three most highly expressed OBP genes (CvesOBP17/18/19) in female antennae demonstrate that they are likely involved in parasitic processes of female wasps, as the wasps take a longer time to target the hosts when they are knocked down.

The complete mitochondrial genome of Trichopria drosophilae (Hymenoptera: Diapriidae).

Trichopria drosophilae (Hymenoptera: Diapriidae) is an important pupal endoparasitoid of Drosophila species, which has been found to be an ideal biocontrol agent to D. suzukii. In this study, the complete mitochondrial genome of T. drosophilae (GeneBank accession number: MN966974) was sequenced using Illumina HiSeq X Ten system. The mitochondrial genome is 16,375 bp long and comprises 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. Among them, 24 genes are in majority strand, while the others are in minority strand. The nucleotide composition of A, G, C, T is 44.9%, 6.4%, 5.6%, 43.2% respectively. We also performed a phylogenetic analysis with other known mitochondrial genomes within four families that have been shown to parasitize drosophilid species. The result shows that T. drosophilae is closely related to Ismarus sp.

Fate of organic micropollutants and their biological effects in a drinking water source treated by a field-scale constructed wetland.

The safety of drinking water is directly related to the occurrence and concentrations of numerous organic micropollutants (OMPs) in source water. In this study, an approach integrating in vitro bioassays and chemical analyses was used to assess the purification effects of a field-scale constructed wetland on the fates of OMPs and their relevant toxicities and health risks in both summer and winter. Overall, 45 of 86 OMPs, including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), organophosphorus pesticides (OPPs), and phthalates (PAEs), were detected in at least one of the water samples. The constructed wetland significantly decreased the concentrations of most types of OMPs, while showed negative effects on the PAEs and OPPs. Toxicological evaluation of water samples indicated that the cytotoxicity, reactive oxygen species (ROS) level and anti-androgen (Ant-AR) activity were all dramatically decreased after the constructed wetland treatment. PAEs and PAHs were the dominant contributors and accounted for 75.12-97.48% of the predicted Ant-AR potencies, while the total predicted Ant-AR potencies only contributed 3.13-15.97% of the observed Ant-AR potencies in the examined water samples, suggesting more OMPs that pose toxic effects are still undetected. The human health risk assessment demonstrated that noncarcinogenic risks of the water samples were acceptable. However, potential carcinogenic risks that were mainly induced by 2, 6-dinitrotoluene, 2, 4-dinitrotoluene, pentachlorophenol and PAEs cannot be ignored. This study can help to understand the role of constructed wetlands in removing OMPs and biological effects from drinking water sources.

The developmental transcriptome of Trichopria drosophilae (Hymenoptera: Diapriidae) and insights into cuticular protein genes.

The pupal endoparasitoid wasp Trichopria drosophilae (Hymenoptera: Diapriidae) plays an important role in biological control of many frugivorous fruit fly species including Drosophila suzukii, a well-known invasive pest. Here, we report the transcriptomes of T. drosophilae among different developmental stages. A total of 601,148,438 high-quality reads were obtained and de novo assembled into 187,704 unigenes with an average length of 1096 bp. Among them, 21,735 unigenes were annotated into 52 Gene Ontology terms and 36,898 were assigned to 25 Cluster of Orthologous Groups categories, whereas 30,585 unigenes were mapped to 270 Kyoto Encyclopedia of Genes and Genomes different pathways. Numbers of differentially expressed genes were found through comparisons between different developmental stages. We further identified 137 cuticular protein genes (CPs) from T. drosophilae transcriptome, including 59 from CPR family, 2 from Tweedle family, 1 from CPF family, 46 from CPAP family, and 29 from other CP families. We analyzed expression patterns of the CPs at different developmental stages of T. drosophilae, and found some stage-specific CPs. Quantitative real-time PCR results confirmed RNA sequencing findings based on the relative expression levels of eight randomly selected CPs. This study provides a valuable transcriptomic resource for a comprehensive understanding of the development and physiology of T. drosophilae, and will help to improve their parasitism efficiency for biological control purposes.

Hybrid of Fe3C@N, S co-doped carbon nanotubes coated porous carbon derived from metal organic frameworks as an efficient catalyst towards oxygen reduction.

High cost, low reserves and poor stability of the Pt-based catalysts have hindered their large-scale applications. To solve these problems, we develop an efficient method to fabricate a hybrid of Fe3C@N, S co-doped carbon nanotubes coated porous carbon as a superior catalyst towards ORR. The resulted Fe-N-S/C sample exhibits excellent performance in alkaline solution, with a half-wave potential of 0.89 V, which is 30 mV higher than that of commercial Pt/C. The electron transfer number is 3.9 at 0.4 V, indicating a direct four-electron (4e-) pathway towards ORR, and the kinetic current density Jk is 7.96 mA cm-2 at 0.88 V. After 5000 repeated potential cycling test, only 4 mV of down-shift in its half-wave potential was detected, which manifested the remarkable stability of Fe-N-S/C. The electrochemical performance is attributed to the ordered porous structure, high content of active N-species and the synergistic effect between Fe3C group and S dopants.

Metal-organic frameworks-derived core-shell Fe3O4/Fe3N@graphite carbon nanocomposites as excellent non-precious metal electrocatalyst for oxygen reduction.

Metal-organic frameworks (MOFs), as precursors for synthesizing new carbon materials, hold promise for applications in the oxygen reduction reaction (ORR) as efficient non-precious metal catalysts. Here, a facile template-assisted strategy was adopted to fabricate a core-shell structure derived from MIL-101(Fe) and polyaniline. MIL-101(Fe) nanoparticles obtained by microwave-assisted synthesis were combined with PAni in different ratios and carbonized at 900 °C under flowing N2. An optimized core-shell Fe3O4/Fe3N@graphite carbon structure was successfully prepared and exhibited attractive ORR activity, with a half-wave potential of 0.916 V vs. RHE and an electron transfer number of 4.0 at 0.4 V vs. RHE. Furthermore, the catalyst displayed excellent stability in an alkaline solution. The superior ORR performance of the catalyst is mainly attributed to its stable core-shell structure, large specific surface area and high content of electrocatalytically active N species.