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Simple Summary: Sipunculus nudus is a species of significant economic importance because of its high nutritional and medicinal value. It is widely distributed along coastlines worldwide, particularly in China, where a comprehensive industry exists encompassing breeding, farming, processing, and sale. Traditionally, S. nudus is cultured on sandy beaches without the need for artificial diets. The organisms rely on nutrients from the surface sediment, including microalgae and other organic matter. These worms inhabit both the intertidal and subtidal zones, enduring varying immersion periods throughout their growth process. As a result, they are exposed to different abiotic factors, such as varying irradiation times, oxygen availability, and others. In our study, we investigated the transcriptomic response of S. nudus across high, middle, and low tidal flats. We analyzed and compared the differential gene expression and relevant metabolic pathways in S. nudus from different habitats. This analysis aimed to shed light on the molecular mechanisms underpinning physiological responses to diverse environments in burrowing species. Interestingly, we observed that the differential gene expression of S. nudus primarily involved metabolic pathways associated with disease and immune responses rather than thermal stress, calcification, and pH regulation. This finding highlights the close relationship between gene expression and S. nudus' unique living habits The peanut worm (Sipunculus nudus) is an important intertidal species worldwide. Species living in the same aquaculture area might suffer different environmental impacts. To increase knowledge of the molecular mechanisms underlying the response to environmental fluctuations, we performed a transcriptome analysis of S. nudus from different intertidal zones using a combination of the SMRT platform and the Illumina sequencing platform. (1) A total of 105,259 unigenes were assembled, and 23,063 unigenes were perfectly annotated. The results of the PacBio Iso-Seq and IIIumina RNA-Seq enriched the genetic database of S. nudus. (2) A total of 830 DEGs were detected in S. nudus from the different groups. In particular, 33 DEGs had differential expression in the top nine KEGG pathways related to pathogens, protein synthesis, and cellular immune response and signaling. The results indicate that S. nudus from different zones experience different environmental stresses. (3) Several DEGs (HSPA1, NFKBIA, eEF1A, etc.) in pathways related to pathogens (influenza A, legionellosis, measles, and toxoplasmosis) had higher expression in groups M and L. HSPA1 was clearly enriched in most of the pathways, followed by NFKBIA. The results show that the peanut worms from the M and L tidal flats might have suffered more severe environmental conditions. (4) Some DEGs (MKP, MRAS, and HSPB1) were upregulated in peanut worms from the H tidal flat, and these DEGs were mainly involved in the MAPK signaling pathway. These results indicate that the MAPK pathway may play a vital role in the immune response of the peanut worm to the effects of different intertidal flats. This study provides a valuable starting point for further studies to elucidate the molecular basis of the response to different environmental stresses in S. nudus. [ABSTRACT FROM AUTHOR]

Simple Summary: The interactions between parasitoids and their host have always attracted much attention, and parasitoids manipulate the host physiology to benefit the survival and development of their offspring. It is critical to analyze these physiological regulatory mechanisms. In this study, using RNA-sequencing analysis, we clarified the effects of parasitization on host gene expression of Microplitis manilae, a dominant larval parasitoid of Spodoptera frugiperda. Several differentially expressed genes were identified in S. frugiperda larvae at 2 h, 24 h, and 48 h post-parasitization. Among these, many genes were implicated in host metabolism and immunity. Further qPCR results involving 20 differentially expressed metabolism, and immune-related genes were consistent with the expression profiles of the RNA-seq data, which confirmed the physiological manipulation of M. manilae on host S. frugiperda. These results contribute to defining the molecular basis of wasps' successful parasitization and facilitate their application. It has been extensively found that parasitoids manipulate host physiology to benefit the survival and development of their offspring. However, the underlying regulatory mechanisms have not received much attention. To reveal the effects of parasitization of the larval solitary endoparasitoid Microplitis manilae (Hymenoptera: Braconidae) on host Spodoptera frugiperda (Lepidoptera: Noctuidae), one of the most destructive agricultural pests in China, deep-sequencing-based transcriptome analysis was conducted to compare the host gene expression levels after 2 h, 24 h, and 48 h parasitization. A total of 1861, 962, and 108 differentially expressed genes (DEGs) were obtained from the S. frugiperda larvae at 2 h, 24 h, and 48 h post-parasitization, respectively, compared with unparasitized controls. The changes in host gene expressions were most likely caused by the injection of wasp parasitic factors, including PDVs, that were injected along with the eggs during oviposition. Based on the functional annotations in GO and KEGG databases, we revealed that most DEGs were implicated in host metabolism and immunity. Further analysis of the common DEGs in three comparisons between the unparasitized and parasitized groups identified four genes, including one unknown and three prophenoloxidase (PPO) genes. Moreover, 46 and 7 common DEGs involved in host metabolism and immunity were identified at two or three time points after parasitization, respectively. Among these, most DEGs showed increased expressions at 2 h post-wasp parasitization while exhibiting significantly decreased expression levels at 24 h post-parasitization, demonstrating the expression regulations of M. manilae parasitization on host metabolism and immune-related genes. Further qPCR verification in 20 randomly selected DEGs confirmed the accuracy and reproducibility of the gene expression profiles generated from RNA-seq. This study reveals the molecular regulatory network about how host insects respond to wasp parasitism, laying a solid foundation for revealing the physiological manipulation of wasp parasitization on host insects, which facilitates the development of biological control practices for parasitoids. [ABSTRACT FROM AUTHOR]

Nitrogen (N 2)-fixing legumes can be used for phytoremediation of toxic heavy metal Mercury (Hg) contaminated soil, but N 2 -fixation highly relies on phosphorus (P) availability for nodule formation and functioning. Here, we characterized the significance of P deficiency for Hg accumulation and toxicity in woody legume plants. Consequences for foliar and root traits of rhizobia inoculation, Hg exposure (+Hg) and low P (-P) supply, individually and in combination were characterized at both the metabolite and transcriptome levels in seedlings of two Robinia pseudoacacia L. provenances originating from contrasting climate and soil backgrounds, i.e., GS in northwest and the DB in northeast China. Our results reveal that depleted P mitigates the toxicity of Hg at the transcriptional level. In leaves of Robinia depleted P reduced oxidative stress and improved the utilization strategy of C, N and P nutrition; in roots depleted P regulated the expression of genes scavenging oxidative stress and promoting cell membrane synthesis. Rhizobia inoculation significantly improved the performance of both Robinia provenances under individual and combined +Hg and -P by promoting photosynthesis, increasing foliar N and P content and reducing H 2 O 2 and MDA accumulation despite enhanced Hg uptake. DB plants developed more nodules, had higher biomass and accumulated higher Hg amounts than GS plants and thus are suggested as the high potential Robinia provenance for future phytoremediation of Hg contaminated soils with P deficiency. Soil pollution and nutrient depletion constitute serious threats for human and environmental health. However, information on the responses of plants to combined Hg pollution and P depletion has so far not been reported, at both, the metabolite and transcriptome levels. In the present study, we characterized the interaction of Hg exposure with P depletion in Robinia -rhizobia associations of two Robinia provenances originating from different environments at the metabolic and transcriptional levels. Provenance-specific differences in Robinia performance upon rhizobia inoculation at Hg and low P exposure were identified. From these results we recommend one of the two Robinia provenances for future remediation of Hg contaminated soils with low P content. [Display omitted] • P depletion showed antagonistic effects when combined with Hg exposure on Robinia-rhizobia symbiosis. • Rhizobia inoculation improved plant performance under combined Hg and depleted P. • Provenance-specific responses of Robinia plants. • Mechanisms in physiological and transcriptional levels were reported. • The DB provenance is feasible than GS for phytoremediation of Hg exposure in P-depleted soil. [ABSTRACT FROM AUTHOR]

Clematis crassifolia and Clematis cadmia Buch.-Ham. ex Hook.f. & Thomson are herbaceous vine plants native to China. C. crassifolia is distributed in shaded areas, while C. cadmia mostly grows in bright, sunny conditions in mountainous and hilly landscapes. To understand the potential mechanisms involved in the irradiance responses of C. crassifolia and C. cadmia, we conducted a pot experiment under three irradiance treatments with natural irradiation and two different levels of shading. Various growth, photosynthetic, oxidative and antioxidative parameters and the relative expression of irradiance-related genes were examined. In total, 15 unigenes were selected for the analysis of gene expression. The exposure of C. crassifolia to high irradiance resulted in growth inhibition coupled with increased levels of chlorophyll, increased catalase, peroxidase, and superoxide dismutase activity and increased expression of c144262_g2, c138393_g1 and c131300_g2. In contrast, under high irradiance conditions, C. cadmia showed an increase in growth and soluble protein content accompanied by a decrease in the expression of c144262_g2, c133872_g1, and c142530_g1, suggesting their role in the acclimation of C. cadmia to a high-irradiance environment. The 15 unigenes were differentially expressed in C. crassifolia and C. cadmia under different irradiance conditions. Thus, our study revealed that there are essential differences in the irradiance adaptations of C. crassifolia and C. cadmia due to the differential physiological and molecular mechanisms underlying their irradiance responses, which result from their long-term evolution in contrasting habitats. [ABSTRACT FROM AUTHOR]

The oriental river prawn, Macrobrachium nipponense, is an important commercial aquaculture resource in China. In order to overwinter, M. nipponense displays decreased physiological activity and less consumption of energy. Sudden warming would trigger molting and cause an extensive death, resulting in huge economic losses. Therefore, it is of great practical significance to study the molting mechanism of oriental river prawns. Molt-inhibiting hormone gene (MIH) plays a major role in regulating molting in crustaceans. In this study, a full length MIH cDNA of M. nipponense (Mn-MIH) was cloned from the eyestalk. The total length of the Mn-MIH was 925 bp, encoding a protein of 119 amino acids. Tissue distribution analysis showed that Mn-MIH was highly expressed in the eyestalk, and that it had relatively low expression in gill, ovary, and abdominal ganglion. Mn-MIH was detected in all developmental stages, and changed regularly in line with the molting cycle of the embryo and larva. Mn-MIH varied in response to the molting cycle, suggesting that Mn-MIH negatively regulates ecdysteroidogenesis. Mn-MIH inhibition by RNAi resulted in a significant acceleration of molting cycles in both males and females, confirming the inhibitory role of MIH in molting. After long-term RNAi males, but not females had significant weight gain, confirming that Mn-MIH plays an important role in growth of M. nipponense. Our work contributes to a better understanding of the role of Mn-MIH in crustacean molting and growth. [ABSTRACT FROM AUTHOR]

Optimal plant density and nitrogen (N) application rate are important to achieve high maize yield. High plant density increases plant-plant competition for light and nutrients. However, too much applied N promotes excessive vegetative growth and delays maturity, resulting in low N use efficiency (NUE) and potentially environmental problems. The physiological and molecular mechanisms behind the interaction between plant density and N application rate are largely unknown. We hypothesized that simultaneously improving maize yield and NUE depends on fine regulation of nitrogen partitioning in response to the interaction between nitrogen applications and plant densities. With a 2-year field experiment, we performed phenotypic, physiological, and gene expression analyses under two plant densities (low density of 60,000 plants ha-1 and high density of 90,000 plants ha-1) and three nitrogen application levels [115 (N1), 190 (N3) and 430 (N4) kg N ha-1] in the high N-responsiveness maize cultivar ZD958. By labeling maize with 15N, 2-year results showed that both 15N uptake per plant and 15N partitioning to ear decreased under high-density conditions. Compared to N1 treatment, application of N to N3/N4 level increased maize yield by 13.9%− 43.2%, which can be explained by bigger root angle, larger leaf area and lower lodging rate under high density condition. In addition, results in 2019 experiment showed that yield, NUE, nitrogen allocation to stem and the expression of some N transporter genes were regulated by the interaction between nitrogen applications and plant densities. Compared to the N4 treatment, N3 treatment has a 55.8% reduction in N, a tendency of increase in population yield, and increased NUE by 59.6% and 63.0% in low-density and high-density plantings, respectively. Our proposed model suggested that the appropriate N supply increased NUE by either increasing N translocation from leaves to ears under low-density conditions or by increasing N allocation to ears rather than to stems under high-density conditions. Based on correlation analysis, N allocation/translocation and expression of nitrogen transporter genes could be used as biomarkers to indicate appropriate levels of N application under different planting densities, and are thereby important for the simultaneously improving ZD958 yield and NUE in intensive agriculture. [ABSTRACT FROM AUTHOR]

The grass carp (Ctenopharyngodon idella) is an important commercial farmed herbivorous fish species in China, but is susceptible to Aeromonas hydrophila infections. In the present study, we performed de novo RNA-Seq sequencing of spleen tissue from specimens of a disease-resistant family, which were given intra-peritoneal injections containing PBS with or without a dose of A. hydrophila. The fish were sampled from the control group at 0 h, and from the experimental group at 4, 8, 12, 24, 48 and 72 h. 122.18 million clean reads were obtained from the normalized cDNA libraries; these were assembled into 425,260 contigs and then 191,795 transcripts. Of those, 52,668 transcripts were annotated with the NCBI Nr database, and 41,347 of the annotated transcripts were assigned into 90 functional groups. 20,569 unigenes were classified into six main categories, including 38 secondary KEGG pathways. 2,992 unigenes were used in the analysis of differentially expressed genes (DEGs). 89 of the putative DEGs were related to the immune system and 41 of them were involved in the complement and coagulation cascades pathway. This study provides insights into the complement and complement-related pathways involved in innate immunity, through expression profile analysis of the genomic resources in C. idella. We conclude that complement and complement-related genes play important roles during defense against A. hydrophila infection. The immune response is activated at 4 h after the bacterial injections, indicating that the complement pathways are activated at the early stage of bacterial infection. The study has improved our understanding of the immune response mechanisms in C. idella to bacterial pathogens. [ABSTRACT FROM AUTHOR]

Primary objective: Lipopolysaccharide (LPS) is known to alter the integrity of the blood-brain barrier (BBB) in sepsis, although the underlying mechanism remains unknown. The aim of this study was to elucidate the molecular mechanisms underlying disruption of the BBB in LPS-induced sepsis. Research design: Both in vitro and in vivo experiments were designed to test the role of AMP-activated protein kinase (AMPK) in LPS-induced BBB dysfunction. Methods and procedures: Human brain microvascular endothelial cells (HBMECs) were cultured. The protein expressions were detected by western blot. BBB integrity was determined by Evans Blue. Main outcomes and results: LPS (1 μg ml-1) dramatically increased the permeability of the BBB and the ROS productions, as well as reducing the expression levels of occludin and claudin-5 in cultured HBMECs. Inhibition of NAD(P)H oxidase by apocynin or up-regulation of AMPK reversed the LPS-induced abnormities in HBMECs. In LPS-induced sepsis in mice, it was found that LPS dramatically increased NAD(P)H oxidase protein expressions and ROS productions in the brain and disrupted BBB function assayed by Evans blue staining, which were abolished by AICAR treatment. Conclusions: It is concluded that AMPK activation improves the functions of the BBB impaired by LPS through suppression of NAD(P)H oxidase-derived ROS in mice. [ABSTRACT FROM AUTHOR]

The Huoyan goose is famous for its high egg-laying performance and is listed as a nationally protected domestic animal by the Chinese government. To elucidate the key regulatory genes involved in Huoyan goose egg laying, RNA from ovarian tissue during the ceased and laying periods was sequenced using the Illumina HiSeq 2000 sequencing platform. More than 12 million reads were produced in ceased and laying libraries that included 11,896,423 and 12,534,799 clean reads, respectively. More than 20% of the reads were matched to the reference genome, and 23% of the reads were matched to reference genes. Genes with a false discovery rate (FDR) ≤0.001 and log2ratio ≧1 or ≤−1 were characterized as differentially expressed, and 344 up-regulated and 344 down-regulated genes were classified into functional categories. Twelve genes that are mainly involved in pathways for reproduction regulation, such as steroid hormone biosynthesis, GnRH signaling pathways, oocyte meiosis, progesterone-mediated oocyte maturation, steroid biosynthesis, calcium signaling pathways, and G-protein coupled receptor signaling pathway were selected for validation by a quantitative real-time polymerase chain reaction (qRT-PCR) analysis, the qRT-PCR results are consistent with the general expression patterns of those genes from the Illumina sequencing. These data provide comprehensive gene expression information at the transcriptional level that might increase our understanding of the Huoyan goose's reproductive biology. [ABSTRACT FROM AUTHOR]

In our precious study, the correlation between cold and hot patterns in traditional Chinese medicine (TCM) and gene expression profiles in rheumatoid arthritis (RA) has been explored. Based on TCM theory, deficiency pattern is another key pattern diagnosis among RA patients, which leads to a specific treatment principle in clinical management. Therefore, a further analysis was performed aiming at exploring the characteristic gene expression profile of deficiency pattern and its correlation with cold and hot patterns in RA patients by bioinformatics analysis approach based on gene expression profiles data detected with microarray technology. The TCM deficiency pattern-related genes network comprises 7 significantly, highly connected regions which are mainly involved in protein transcription processes, protein ubiquitination, toll-like receptor activated NF-kB regulated gene transcription and apoptosis, RNA clipping, NF-kB signal, nucleotide metabolism-related apoptosis, and immune response processes. Toll-like receptor activated NF-kB regulated gene transcription and apoptosis pathways are potential specific pathways related to TCM deficiency patterns in RA patients; TCM deficiency pattern is probably related to immune response. Network analysis can be used as a powerful tool for detecting the characteristic mechanism related to specific TCM pattern and the correlations between different patterns. [ABSTRACT FROM AUTHOR]

Aims Hepatocyte nuclear factor-1α (HNF-1α) regulates the expression of genes encoding proteins involved in glucose metabolism and insulin secretion. Mutations in the HNF-1α gene cause maturity-onset diabetes of the young Type 3. However, the mechanism leading to this disease has not been completely ascertained. Previously, we found a novel mutation in the regulatory element of the human HNF-1α gene in two Chinese diabetes pedigrees. The nucleotide at position -128 T was substituted by G (nt-128 T→G). In this study, we analysed the functional defect of nt-128 T→G in HNF-1α transcription activity. Methods Luciferase reporter gene assays were carried out to examine the functional characteristics of this mutant. Electrophoretic mobility shift assays and chromatin immunoprecipitation were performed to confirm the binding of nuclear proteins to oligonucleotides. Results The variant construct (nt-128 T→G) had a 1.65-fold increase in promoter activity compared with that of the wild-type construct in HepG2 cells and a 1.33-fold increase in MIN6 cells, respectively. The variant resided at a FOXA/HNF-3 binding site identified by a series of competitive electrophoretic mobility shift assays and antibody supershift analyses. The assays showed a differential binding affinity in the wild-type and the nt-128 T→G mutant fragments by FOXA/HNF-3. Chromatin immunoprecipitation indicated that FOXA/HNF-3 bound to this region in vivo. One nucleotide substitution in the FOXA/HNF-3 site in the human HNF-1α regulatory element caused an increase of HNF-1α transcriptional activity. Conclusions Our data suggested that this substitution in the promoter region affects DNA-protein interaction and HNF-1α gene transcription. The mutant may contribute to the development of diabetes in these two nt-128 T→G pedigrees of Chinese. [ABSTRACT FROM AUTHOR]

The maize inbred lines Huangzao 4 (HZ4) and Chang 7-2 (C7-2) are the foundation genotypes key to maize cross-breeding in China. C7-2 is derived from HZ-4. In this study, changes in phenotype, physiology and gene expression of three-leaf-old seedlings of HZ4 and C7-2 under the conditions of progressive water deficit (WD) and re-watering (RW) were compared to gain knowledge for breeding new maize foundation genotypes with higher drought tolerance. Progressive WD was produced by adding polyethylene glycol (PEG 6000) at 24 h intervals (24, 48 and 72 h) in Hoagland’s nutrient solution, resulting in water potentials of −0.15, −0.3 and −0.5 MPa. The seedlings treated for 24 h at −0.3 MPa were subjected to RW in the solution without complementation with PEG. The results showed that C7-2 seedlings are more tolerant to progressive WD than HZ4 seedlings in part because the former have a larger stomatal resistance, a relatively stronger leaf water-holding capacity, and a timely and stable increase in activities of antioxidant enzymes (superoxide dismutase and peroxidase) especially in roots upon WD. Oligonucleotide probe array-based analysis uncovered a number of WD- and RW-regulated genes in both inbred lines, and clearly indicated that fine transcriptional coordination between maize leaves and roots is one of the factors constituting higher WD tolerance and a greater ability for growth recovery from WD. On the basis of the resulting data and co-regulation of responsive genes in tissues, we propose a model for the whole maize plant tolerance to growth and recovery from WD. [ABSTRACT FROM PUBLISHER]

• Spraying ABA improved the drought resistance ability of Bupleurum chinense. • Exogenous ABA inhibited the expression of saikosaponin synthesis pathway genes. • Cultivators need to pay attention to the change of ABA in medicinal plants. • Drought can affect molecular mechanisms important for medicinal plant quality. Abscisic acid (ABA) plays an important role in stress resistance and secondary metabolism of plants under drought stress. Bupleurum chinense DC. is a medicinal plant cultivated in arid areas in China. In this study, the effects of progressive drought stress (22 days) and exogenous ABA (5 mg L–1) treatment on plant physiological characteristics and saikosaponin secondary metabolism were investigated in 2-year-old B. chinense. The samples were collected on 6, 10, 14, 18 and 22 days after drought stress (DADS). In drought stressed B. chinense plants treated with ABA, root weight loss and malondialdehyde accumulation was reduced, while drought resistance increased, as indicated by the accumulation of soluble protein and soluble sugar content, and by the increased activities of superoxide dismutase and peroxidase. At the early stage of drought stress (first 6 days), saikosaponin increased more sharply in plants exposed to drought stress and its accumulation indicated increased sensitivity to this condition. At this time, saikosaponin content reached 31.83 mg g−1, which was 33.6 % higher than that in control plants. Using principal component analysis and fuzzy membership function calculation, comprehensive evaluation values of gene expression in the drought (D) and D + ABA treated groups at different drought exposure time were evaluated. Exogenous ABA inhibited the expression of saikosaponin biosynthesis-related genes from 6 to 14 DADS of drought stress. However, gene expression was up-regulated at later stages of drought stress (the 22 DADS), while genes involved in saikosaponin content were down-regulated in the D group compared with those in the D + ABA group. Indeed, saikosaponin content in both of these groups was significantly higher than that in the control group. Correlation analysis suggested that the expression of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) gene was positively correlated with total saikosaponin (SSs) (p < 0.01), and saikosaponin a (SS-a) and saikosaponin d (SS-d) (p < 0.05) content, while that of farnesyl pyrophosphate synthase (FPS) gene was positively correlated with SSs (p < 0.05), and SS-a and SS-d (p < 0.01) content in the D group. These results indicated that HMGR and FPS play a key role in saikosaponin biosynthesis during drought stress. Moreover, the negative correlations between multiple genes and saikosaponin after ABA treatment [particularly that of cytochrome P450−7 with SS-d (p < 0.01) and glycosyl transferase-8 with SS-d (p < 0.05)], indicated that exogenous ABA reduced saikosaponin accumulation by inhibiting the expression of saikosaponin biosynthesis-related genes in B. chinense exposed to drought stress. This study provides new insight into the effect of ABA on secondary metabolism and it will be of great importance to cultivators and researchers aiming to understand how ABA application affects medicinal plant cultivation. [ABSTRACT FROM AUTHOR]