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ABSTRACT Fine-tuning the expression level of an engineered pathway is crucial for the metabolic engineering of a host toward a desired phenotype. However, most engineered hosts suffer from nonfunctional protein expression, metabolic imbalance, cellular burden or toxicity from intermediates when an engineered pathway is first introduced, which can decrease production of the desired product. To circumvent these obstacles, we developed a self-regulation system utilizing the trc/ tac promoter, LacIq protein and ribosomal binding sites (RBS). With the purpose of improving coenzyme Q10 (CoQ10) production by increasing the decaprenyl diphosphate supplement, enzymes DXS, DXR, IDI, and IspD were constitutively overexpressed under the control of the trc promoter in Rhodobacter sphaeroides. Then, a self-regulation system combining a set of RBSs for adjusting the expression of the LacIq protein was applied to tune the expression of the four genes, resulting in improved CoQ10 production. Finally, another copy of the tac promoter with the UbiG gene (involved in the ubiquinone pathway of CoQ10 biosynthesis) was introduced into the engineered pathway. By optimizing the expression level of both the upstream and downstream pathway, CoQ10 production in the mutants was improved up to 93.34 mg/L (7.16 mg/g DCW), about twofold of the wild-type (48.25 mg/L, 3.24 mg/g DCW). Biotechnol. Bioeng. 2014;111: 761-769. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

ABSTRACT Saccharomyces cerevisiae is an important platform organism for the synthesis of a great number of natural products. However, the assembly of controllable and genetically stable heterogeneous biosynthetic pathways in S. cerevisiae still remains a significant challenge. Here, we present a strategy for reconstructing controllable multi-gene pathways by employing the GAL regulatory system. A set of marker recyclable integrative plasmids (pMRI) was designed for decentralized assembly of pathways. As proof-of-principle, a controllable β-carotene biosynthesis pathway (∼16 kb) was reconstructed and optimized by repeatedly using GAL10- GAL1 bidirectional promoters with high efficiency (80-100%). By controling the switch time of the pathway, production of 11 mg/g DCW of total carotenoids (72.57 mg/L) and 7.41 mg/g DCW of β-carotene was achieved in shake-flask culture. In addition, the engineered yeast strain exhibited high genetic stability after 20 generations of subculture. The results demonstrated a controllable and genetically stable biosynthetic pathway capable of increasing the yield of target products. Furthermore, the strategy presented in this study could be extended to construct other pathways in S. cerevisisae. Biotechnol. Bioeng. 2014;111: 125-133. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Excessive hepatic lipid accumulation is a common phenomenon in cultured fish; however, its underlying mechanisms are poorly understood. Lipid droplet (LD)-related proteins play vital roles in LD accumulation. Herein, using a zebrafish liver cell line (ZFL), we show that LD accumulation is accompanied by differential expression of seven LD-annotated genes, among which the expression of dehydrogenase/reductase (SDR family) member 3 a/b (dhrs3a/b) increased synchronously. RNAi-mediated knockdown of dhrs3a delayed LD accumulation and downregulated the mRNA expression of peroxisome proliferator-activated receptor gamma (pparg) in cells incubated with fatty acids. Notably, Dhrs3 catalyzed retinene to retinol, the content of which increased in LD-enriched cells. The addition of exogenous retinyl acetate maintained LD accumulation only in cells incubated in a lipid-rich medium. Correspondingly, exogenous retinyl acetate significantly increased pparg mRNA expression levels and altered the lipidome of the cells by increasing the phosphatidylcholine and triacylglycerol contents and decreasing the cardiolipin, phosphatidylinositol, and phosphatidylserine contents. Administration of LW6, an hypoxia-inducible factor 1α (HIF1α) inhibitor, reduced the size and number of LDs in ZFL cells and attenuated hif1αa, hif1αb, dhrs3a, and pparg mRNA expression levels. We propose that the Hif-1α/Dhrs3a pathway participates in LD accumulation in hepatocytes, which induces retinol formation and the Ppar-γ pathway. [ABSTRACT FROM AUTHOR]

Current studies on microbial isoprene biosynthesis have mostly focused on regulation of the upstream mevalonic acid (MVA) or methyl-erythritol-4-phosphate (MEP) pathway. However, the downstream bottleneck restricting isoprene biosynthesis capacity caused by the weak expression and low activity of plant isoprene synthase (ISPS) under microbial fermentation conditions remains to be alleviated. Here, based on a previously constructed Saccharomyces cerevisiae strain with enhanced precursor supply, we strengthened the downstream pathway through increasing both the expression and activity of ISPS to further improve isoprene production. Firstly, a two-level expression enhancement system was developed for the P GAL1 -controlled ISPS by overexpression of GAL 4 . Meanwhile, the native GAL1 /7/10 promoters were deleted to avoid competition for the transcriptional activator Gal4p, and GAL80 was disrupted to eliminate the dependency of gene expression on galactose induction. The IspS expression was obviously elevated upon enhanced Gal4p supply, and the isoprene production was improved from 6.0 mg/L to 23.6 mg/L in sealed-vial cultures with sucrose as carbon source. Subsequently, a novel high-throughput screening method was developed based on precursor toxicity and used for ISPS directed evolution towards enhanced catalytic activity. Combinatorial mutagenesis of the resulting ISPS mutants generated the best mutant ISPSM4, introduction of which into the GAL4 -overexpressing strain YXM29 achieved 50.2 mg/L of isoprene in sealed vials, and the isoprene production reached 640 mg/L and 3.7 g/L in aerobic batch and fed-batch fermentations, respectively. These results demonstrated the effectiveness of the proposed combinatorial engineering strategy in isoprene biosynthesis, which might also be feasible and instructive for biotechnological production of other valuable chemicals. [ABSTRACT FROM AUTHOR]

Improper fertilization or excessive nitrogen input may cause serious environmental problems and affect soil health. This is particularly the case in saline agroecosystems, as soil salinization alters nitrogen cycling and contributes to substantial nitrogen losses. However, the impact of amendment materials on the combined processes of nitrogen transformation and migration in salt-affected soil has not yet been explicitly clarified. Here, soil column and incubation experiments on biochar (BC)- and potassium humate (PH)-amended salt-affected soil were conducted. The transport and redistribution characteristics of soil water, salt and mineral nitrogen under drip fertigation (urea as fertilizer) were investigated, and the responses of urea hydrolysis and nitrification to BC and PH addition under soil salinity gradients were elucidated. The results showed that BC application increased the migration and redistribution ranges of soil water, salt and mineral nitrogen by improving soil macropores and infiltration and diffusion rates. PH addition maintained higher contents of soil water, salt and mineral nitrogen in the wetting pattern by enhancing the soil water-holding capacity. Both BC and PH addition shifted not only the transport and redistribution but also the morphological conversion of urea-N. BC and PH addition delayed the rise and decline of ammonium nitrogen (NH4+-N) content and postponed the rise of nitrate-nitrogen (NO3−-N) content in the wetting pattern. The results of the incubation experiment corroborated those of the column experiment. Both BC and PH aggravated the inhibitory effect of soil salinity on urea hydrolysis and nitrification by prolonging the duration by 2–7 days and postponing the time when the maximum NH4+-N and NO3−-N concentrations were reached. PH showed a stronger inhibitory effect on nitrification than BC. The redistribution of urea-N in soil under drip fertigation was primarily dominated by water migration and diffusion, as physically mediated by BC and PH addition, and by the morphological conversion biochemically affected by the interactions of soil salt and BC and PH addition. It was concluded that morphological conversion played an important role in soil nitrogen transport and redistribution, and it is essential to consider the interactive impact of amendment materials and soil salinity level on nitrogen transformation for efficient and sustainable management of fertilizer nitrogen in salt-affected soil. [ABSTRACT FROM AUTHOR]

Huntington's disease (HD) is a neurodegenerative disease. MicroRNAs (miRNAs) are small non-coding RNAs that mediate post-transcriptional regulation of target genes. Although miRNAs are extensively edited in human brains, the editome of miRNAs in brains of HD patients is largely unknown. By analyzing the small RNA sequencing profiles of brain tissues of 28 HD patients and 83 normal controls, 1182 miRNA editing sites with significant editing levels were identified. In addition to 27 A-to-I editing sites, we identified 3 conserved C-to-U editing sites in miRNAs of HD patients. 30 SNPs in the miRNAs of HD patients were also identified. Furthermore, 129 miRNA editing events demonstrated significantly different editing levels in prefrontal cortex samples of HD patients (HD-PC) when compared to those of healthy controls. We found that hsa-mir-10b-5p was edited to have an additional cytosine at 5'-end in HD-PC, and the edited hsa-mir-10b repressed GTPBP10 that was often downregulated in HD. The down-regulation of GTPBP10 might contribute to the progression of HD by causing gradual loss of function of mitochondrial. These results provide the first endeavor to characterize the miRNA editing events in HD and their potential functions. [ABSTRACT FROM AUTHOR]

Aims: Soil fungal communities play pivotal roles in promoting ecosystem carbon (C) and nitrogen (N) cycling, stimulating disease resistance and enhancing tolerance against salt stress of host plants. However, the impact of anthropogenic management practices on the soil fungal community structure has not yet been clarified. Methods: Using a four-consecutive-year field experiment and the quantitative polymerase chain reaction (qPCR) and Illumina MiSeq DNA sequencing methods, the single and interactive impacts of crop cultivation (CK), N fertilization (N) and fulvic acid (F) on soil fungal diversity, abundance, composition and functional groups were investigated. Results: Consecutive crop cultivation improved soil chemical and microbial properties by reducing soil electrical conductivity (ECe) and enhancing soil organic carbon (SOC), microbial biomass carbon (MNC), and microbial biomass nitrogen (MBN). Crop cultivation had larger contribution to fungal richness and diversity than N fertilization and fulvic acid. Crop cultivation enriched mycorrhizal fungi and N fertilization enriched endophytic, saprophytic and pathogenic fungi. Structural equation modeling (SEM) revealed that soil ECe and pH indirectly influenced MBN through their adverse direct impact on OTUs, Shannon index and abundance of predominant fungal taxa. N input exhibited a positive indirect influence on MBN through enhancing abundance of Funneliformis at the genus level. Conclusions: Crop cultivation, N input, and fulvic acid addition in saline soil environment changed the environmental niches and drove the evolution of soil fungal community. In return, the shifts in soil fungal community composition and functional groups greatly affected soil C and N transformation with potential feedback on soil microbial activity. [ABSTRACT FROM AUTHOR]

Understanding the impacts of tillage on soil microflora, especially functional microbes related to nitrogen conversion, is essential for ensuring the sustainable production, biodiversity and function of agroecosystems in salinized soils. Based on a two-year field plot experiment in a salt-affected farmland, the effects of three tillage methods, namely, CT (conventional rotary tillage, depth 25 cm), VRT (vertical rotary tillage, depth 25 cm) and DVRT (deep vertical rotary tillage, depth 50 cm), on soil physicochemical properties and ammonia-oxidizing archaea (AOA), bacteria (AOB) and comammox bacteria (CAOB) communities were investigated. Soil samples over the sunflower (Helianthus annuus L.) growing season were collected on three dates, i.e., April 28, July 6, and September 6, 2020. The results indicated that CT, VRT and DVRT had the lowest EC 1:5 values (0.75–1.23 dS/m) and the highest OC (organic carbon, 14.50–19.32 g/kg), WSA1 (> 2 mm water-stable aggregates, 31.05–37.88 g/kg), and WSA2 (2–0.25 mm water-stable aggregates, 69.51–83.70 g/kg) values on the middle sampling date. The average number of OTUs was 51.2 ± 3.3, 43.2 ± 3.8 and 42.8 ± 6.2 (mean ± SD) per soil sample for AOA, AOB and CAOB, respectively. DVRT significantly affected the community richness indices (Sobs, ACE and Chao1) of AOA and AOB, whereas sampling dates shifted almost all the soil physicochemical properties and diversity indices (Shannon and Simpson) of AOA and AOB but not those of CAOB. Phyla Crenarchaeota , unclassified_d_Unclassified , Unclassified_k_norank_d_Archaea and Thaumarchaeota were the most common taxa (with relative abundances >5 %) of AOA under all the treatments. For AOB, >92 % of the taxa were categorized into the phylum Proteobacteria , and CT had a greater frequency of the phylum Proteobacteria than did VRT and DVRT on all sampling dates. For CAOB, approximately 90 % of the taxa were classified into the phylum Nitrospirae , and the relative abundance of Nitrospirae did not differ among the tillage practices, whereas VRT and DVRT had the highest relative abundance of Nitrospirae on the middle sampling date. A total of 88.69 % of the variation in the genus compositions of AOA, AOB and CAOB was explained by EC 1:5 , pH, OC, ρ b (bulk density), WSA1 and WSA2. In conclusion, tillage practices and sampling dates can diversely affect soil physicochemical properties, microbial richness and diversity indices of AOA, AOB and CAOB, and seasonal changes overwhelm tillage practices in shaping AOA, AOB and CAOB communities across the sunflower growing season in salinized irrigated farmland. • Tillage and sampling date dominated richness and diversity, respectively, for AOA and AOB. • Community richness and diversity of CAOB were only responsive to sampling date. • Tillage and seasons affected microbial communities by changing EC 1:5 , pH, OC, ρ b , WSA1 and WSA2. • Seasons overwhelmed tillage in shaping AOA, AOB and CAOB communities in sunflower growing season. [ABSTRACT FROM AUTHOR]

Background and aims: Allogeneic human umbilical mesenchymal stem cells (alloUMSC) are convenient cell source for stem cell-based therapy. However, immune rejection is a major obstacle for clinical application of alloUMSC for cardiac repair after myocardial infarction (MI). The immune rejection is due to the presence of human leukocyte antigen (HLA) class I molecule which is increased during MI. The aim of this study was to knockout HLA light chain β2-microglobulin (B2M) in UMSC to enhance stem cell engraftment and survival after transplantation. Methods and results: We developed an innovative strategy using CRISPR/Cas9 to generate UMSC with B2M deletion (B2M–UMSC). AlloUMSC injection induced CD8+ T cell-mediated immune rejection in immune competent rats, whereas no CD8+ T cell-mediated killing against B2M–UMSC was observed even when the cells were treated with IFN-γ. Moreover, we demonstrate that UMSC-derived exosomes can inhibit cardiac fibrosis and restore cardiac function, and exosomes derived from B2M–UMSC are more efficient than those derived from UMSC, indicating that the beneficial effect of exosomes can be enhanced by modulating exosome's imprinting. Mechanistically, microRNA sequencing identifies miR-24 as a major component of the exosomes from B2M–UMSCs. Bioinformatics analysis identifies Bim as a putative target of miR-24. Loss-of-function studies at the cellular level and gain-of-function approaches in exosomes show that the beneficial effects of B2M–UMSCs are mediated by the exosome/miR-24/Bim pathway. Conclusion: Our findings demonstrate that modulation of exosome's imprinting via B2M knockout is an efficient strategy to prevent the immune rejection of alloUMSCs. This study paved the way to the development of new strategies for tissue repair and regeneration without the need for HLA matching. [ABSTRACT FROM AUTHOR]

The mechanism underlying the efficacy of different bile acids (BAs) as feed additives to prevent or treat fatty liver disease in cultured fish remains poorly understood. This study compared the effect of different types of BAs on farnesoid X receptor (FXR) activity and lipid accumulation in grass carp. A survey revealed that grass carp (608.24 ± 17.511 g) with severe fatty liver had impaired FXR activity and increased liver total bile acids (TBA) content. In an in vitro study, four typical BAs, chenodeoxycholic acid (CDCA), cholic acid (CA), lithocholic acid (LCA), and deoxycholic acid (DCA), were found to significantly upregulate the expression of FXR and small heterodimer partner (SHP) and decreased lipid droplet accumulation in the hepatocytes of grass carp. Among these, DCA and CDCA exerted the most significant effects. In an in vivo study, grass carp (6.29 ± 0.05 g) were fed 100 mg/kg CDCA, CA, LCA, and DCA for 8 weeks; DCA alone significantly reduced lipid content in the liver and total cholesterol (T-CHO), triglyceride (TG), low density lipoprotein cholesterol (LDL-C) and high density lipoprotein cholesterol (HDL C) content in the serum. In addition, DCA improved the lipid catabolic activity, inhibited the lipid anabolic activity, and alleviated inflammation in the liver. In contrast, LCA, CDCA, and CA had the opposite effect on these indices. Mechanistically, DCA had a dominant impact on activating FXR in the liver, whereas the other BAs either inhibited gut FXR activity or had the risk in damaging liver cells. In conclusion, our results suggest that different BAs have varying effects on regulating fat accumulation, and DCA appears to be a particularly effective BA in suppressing fat accumulation via FXR pathway activation in the liver of grass crap. • Liver fat accumulation accompanied by impaired FXR activity and increased BA content in the liver of grass carp. • BAs (CA, CDCA, LCA, and DCA) can activate FXR activity and reduce lipid droplets in grass carp hepatocytes. • Only dietary DCA depresses the hepatic lipid accumulation in vivo. • Dietary DCA activates FXR activity in the liver but not in the gut. • Gut FXR trends to be more effective in controlling fat accumulation than liver FXR. [ABSTRACT FROM AUTHOR]

• Feeding grass carp with faba bean conferred them with "crisp" muscle texture. • "Crisp" grass carp muscle is characterized by substantial protein N -glycosylation. • N -glycosylated proteins participate in myogenesis, muscle function, & ECM formation. • N -glycosylation regulation is independent with phosphorylation regulation and protein expression. • These findings lay a foundation for optimizing fish fillet texture & quality. Post-translational protein modification affects muscle physiochemistry. To understand the roles of N- glycosylation in this process, the muscle N- glycoproteomes of crisp grass carp (CGC) and ordinary grass carp (GC) were analyzed and compared. We identified 325 N- glycosylated sites with the NxT motif, classified 177 proteins, and identified 10 upregulated and 19 downregulated differentially glycosylated proteins (DGPs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations revealed that these DGPs participate in myogenesis, extracellular matrix content formation, and muscle function. The DGPs partially accounted for the molecular mechanisms associated with the relatively smaller fiber diameter and higher collagen content observed in CGC. Though the DGPs diverged from the identified differentially phosphorylated proteins and differentially expressed proteins detected in previous study, they all shared similar metabolic and signaling pathways. Thus, they might independently alter fish muscle texture. Overall, the present study provides novel insights into the mechanisms underlying fillet quality. [ABSTRACT FROM AUTHOR]

• Hydrothermal carbonization aqueous product (AP) and modified AP (MAP) were added to compost. • Either AP or MAP did not influence the maturity of experimental composts. • AP-10% increased the total N and humic substances by 12% and 18%, respectively. • Total P and K content were enhanced by 8–9% and 20%, respectively, as MAP addition. • AP and MAP increased the contents of all main components of DOM of mature compost. The aqueous phase (AP) of hydrothermal carbonization is rich in humic substances (HSs), which could influence the poultry manure composting process and the product quality. Here, raw AP and its modified product (MAP) with different nitrogen (N) contents were added into chicken manure composting at low (5%) or high (10%) rate. Results showed that all APs addition decreased the temperature and pH but AP-10% increased total N, HSs, and humic acid (HA) of compost by 12%, 18% and 27%, respectively. MAP applications increased the total phosphorus by 8–9% and MAP-10% enhanced the total potussium content by 20%. Additionally, both AP and MAP additions increased the contents of three major components of dissolved organic matter by 20–64%. In conclusion, both AP and MAP can generally improve the chicken manure compost quality, which provides a new idea for the recycling of APs derived from agro-forestry wastes during hydrothermal carbonization. [ABSTRACT FROM AUTHOR]

Rice grown on Cd-contaminated soil may accumulate Cd in grain, which is extremely harmful to human health. Several managements are developed to reduce the Cd load in rice, while in-situ immobilization by soil amendments has been attractive for its feasibility. Waste-derived hydrochar (HC) has been shown effective at immobilizing Cd in soil. However, potential plant negative effects and huge application amount are crucial to resolving in extensive application of HC. Nitric acid ageing may be an effective method to deal with these problems. In this paper, HC and nitrated hydrochar (NHC) were added to the Cd-contaminated soil at rates of 1% and 2% in a rice-soil column experiment. Results showed that NHC markedly promoted root biomass of rice by 58.70–72.78%, whereas HC had effects of 35.86–47.57%. Notably, NHC at 1% reduced the accumulation of Cd in rice grain, root and straw by 28.04%, 15.08% and 11.07%, respectively. A consistent decrease of 36.30% in soil EXC-Cd concentration was caused by NHC-1%. Following soil microbial community was shifted greatly under HC and NHC applications. The relative abundance of Acidobacteria was decreased by 62.57% in NHC-2% and by 56.89% in HC-1%. Nevertheless, Proteobacteria and Firmicutes were promoted by NHC addition. In contrast to HC, co-occurrence network of dominated bacteria was more complex and centralized generated by NHC. Key bacteria in that metabolic network of NHC such as Anaerolineae and Archangiaceae played key roles in Cd immobilization. These observations verified that NHC was more efficient to decrease Cd accumulation in rice and could alleviate the negative roles to plant by microbial changings in community composition and network. It could provide an enrichment of paddy soil microbial responds to the interaction of NHC with Cd and lay a foundation for the remediation of Cd-contaminated soil by NHC. [Display omitted] • Root biomass of rice was promoted by 58.70–72.78% under NHC compared to CK. • NHC reduced grain Cd content by 26.84%–28.04% relative to CK. • Exchangeable Cd in soil was transformed to a more stable form under NHC. • Soil bacterial diversity, composition and network were different from NHC to HC. • Microbial families responded significantly to Cd morphology in paddy soils. [ABSTRACT FROM AUTHOR]

Limited toxicological information is available for hexabromocyclododecane (HBCD),a widely used additive brominated flame retardant. Inhalation is a major route of human exposure to HBCD. The aim of this study was to determine the acute inhalation toxicity and potential subchronic inhalation toxicity of HBCD in Sprague-Dawley rats exposed to HBCD only through inhalation. The acute inhalation toxicity of HBCD was determined using the limit test method on five male and five female Sprague-Dawley rats at a HBCD concentration of 5000 mg/m 3 . Repeated-dose toxicity tests were also performed, with 20 males and 20 females randomly assigned to four experimental groups (five rats of each sex in each group). There were three treatment groups (exposed to HBCD concentrations of 125,500, and 2000 mg/m 3 ) and a blank control group (exposed to fresh air). In the acute inhalation toxicity study, no significant clinical signs were observed either immediately after exposure or during the recovery period. Gross pathology examination revealed no evidence of organ-specific toxicity in any rat. The inhalation LC 50(4 h) for HBCD was higher than 5312 ± 278 mg/m3 for both males and females. In the repeated dose inhalation study, daily head/nose-only exposure to HBCD at 132 ± 8.8, 545.8 ± 35.3, and 2166.0 ± 235.9 mg/m 3 for 14 days caused no adverse effects. No treatment-related clinical signs were observed at any of the test doses. The NOAEL for 14-day repeated dose inhalation toxicity study of HBCD is 2000 mg/m 3 . [ABSTRACT FROM AUTHOR]

Hydrothermal carbonization is an emerging and efficient technology for utilizing wet waste. However, the utilization of hydrothermal carbonization aqueous phase (HAP), a carbon-rich liquid product containing massive quantities of nutrient elements, has been largely unexplored. In this study, HAP produced by hydrothermal carbonization of sewage sludge (SHAP) and pig manure (PHAP) at 180 °C and 260 °C was applied as a substitute for partial (9.1–55.9%) urea in rice paddy field. Results showed that HAP increased the abundance of humic acid-like substances and microbial metabolic by-products in soil dissolved organic matter (DOM) by 3.3–7.2 times and 42.1–101.6%, respectively, compared to the control treatment without HAP addition (CK). Meanwhile, HAP significantly increased soil fluorescence and humification index of soil DOM by 28.5–41.9% and 12.3–26.8%, respectively, in comparison with CK. Soil fertilized with SHAP260 had greater mineral nitrogen, total organic carbon and Olsen-P compared to CK. HAP increased the grain N uptake by 34.0–58.8% and rice yield by 6.3–34.1% with essential amino acids in grains improved by 8.6–20.9% compared to CK. This study stated that HAP as a substitute of partial urea for rice paddy return has positive effects on soil fertility and grain yields. [Display omitted] • Hydrothermal carbonization aqueous phase (HAP) promising substitutes urea as liquid fertilizer. • HAP significantly increased humification index of soil DOM compared to the control. • HAP could increase soil mineral nitrogen and Olsen-P compared to the control. • HAP increased grain essential amino acid by 8.6–20.9% and rice yield by 6.3–34.1%. [ABSTRACT FROM AUTHOR]

[Display omitted] • A method was developed to determine herbicides in sediments and aquatic products. • The method was used for the risk assessment of rice-fish co-culture system in China. • Human health risks of the herbicides were low in paddy field fish (HQ<0.002408). • Five herbicides in the sediment of paddy field showed high ecological risks (RQ>1.0). A sensitive method for determination of nine herbicides (prometryn, acetochlor, butachlor, quinclorac, bensulfuron methyl, metsulfuron methyl, atrazine, linuron and bentazone) in sediments and muscle of aquatic products was developed and validated using QuEChERS and ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). The results demonstrated that the matrix-matched calibration curves for sediment and fish muscle were satisfactory linearly of a concentration (0.50 to 100 μg/L) (r > 0.999). The limit of detection (LOD) and limit of quantification (LOQ) ranged from 0.10 ~ 0.50 μg/kg and 0.50 ~ 1.50 μg/kg, respectively. The recoveries ranged from 82.94 to 114.41%, with the relative standard deviations (RSDs) lower than 13.11% for nine herbicides. Finally, the validated method was applied to detect nine herbicides in 68 rice-fish and 30 sediment samples in the rice-fish co-culture system (RFCS) in six provinces of China. The dietary and ecological risks were evaluated through a calculated hazard quotient (HQ) and risk quotient (RQ). The residues of herbicides in the paddy fish did not harm the human body (HQ < 0.002408). However, the ecological risks of herbicides in the RFCS could not be ignored. The seven herbicides were detected in the sediment of RFCS. They had ecological risks to the fish, daphnia and algae (RQ values ranged from 0.1666 to 28.4381). [ABSTRACT FROM AUTHOR]

The pregnane X receptor (PXR)/nuclear factor-kB (NF-kB) signaling pathway plays a critical role in regulating toxin-induced inflammation and apoptosis in mammals. Whether dietary curcumin (CUR) can prevent copper (Cu)-induced liver injury via this signaling pathway remains to be established in aquatic animals. Juvenile largemouth bass (Micropterus salmoides) were exposed to dietary Cu and CUR treatments for 8 weeks. The results showed that chronic Cu exposure induced oxidative stress, causing liver function damage and liver injury. Cu exposure stimulated inflammation by regulating nf-kb and pro-inflammatory genes such as tnfα and il-1β and promoted apoptotic signals in the liver by modulating bcl2 and casp3 mRNA levels. In addition, Pearson correlation analysis verified that inflammatory and apoptotic responses were important indicators of Cu-induced liver injury. CUR attenuated stress responses by enhancing the antioxidant system. Importantly, CUR significantly stimulated PXR mRNA and protein levels in the Cu + CUR group and suppressed NF-κB activation to inhibit the inflammatory and apoptotic signaling cascade. These results suggest that CUR may be an effective activator of PXR in teleost fishes, exerting cytoprotective effects on Cu-induced liver injury via a PXR-mediated NF-κB repression mechanism. In conclusion, this study is the first to demonstrate that CUR may act as a potent PXR ligand that exerts hepatoprotective effects against Cu-induced liver injury. The findings shed light on the specific regulatory role of the PXR/NF-κB signaling pathway in liver pathogenesis and its potential as a therapeutic target in teleost fishes., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

This study evaluated the treatment efficiency of two selected fillers and their combination for improving the water quality of aquaculture wastewater using a packed bed biofilm reactor (PBBR) under various process conditions. The fillers used were nanosheet (NS), activated carbon (AC), and a combination of both. The results indicated that the use of combined fillers and the hydraulic retention time (HRT) of 4 h significantly enhanced water quality in the PBBR. The removal rates of chemical oxygen demand, NO2-─N, total suspended solids（TSS）, and chlorophyll a were 63.55%, 74.25%, 62.75%, and 92.85%, respectively. The microbiota analysis revealed that the presence of NS increased the abundance of microbial phyla associated with nitrogen removal, such as Nitrospirae and Proteobacteria. The difference between the M1 and M2 communities was minimal. Additionally, the microbiota in different PBBR samples displayed similar preferences for carbon sources, and carbohydrates and amino acids were the most commonly utilized carbon sources by microbiota. These results indicated that the combination of NS and AC fillers in a PBBR effectively enhanced the treatment efficiency of aquaculture wastewater when operated at an HRT of 4 h. The findings provide valuable insights into optimizing the design of aquaculture wastewater treatment systems., (© The Author(s) 2024. Published by Oxford University Press on behalf of Applied Microbiology International.)

Habitual dietary changes have the potential to induce alterations in the host's gut microbiota. Mandarin fish ( Siniperca chuatsi ), an aquatic vertebrate species with distinct feeding habits, were fed with natural feeds (NF) and artificial feeds (AF) to simulate the effects of natural and processed food consumption on host gut microbiota assemblages. The results showed that the alpha diversity index was reduced in the AF diet treatment, as lower abundance and diversity of the gut microbiota were observed, which could be attributed to the colonized microorganisms of the diet itself and the incorporation of plant-derived proteins or carbohydrates. The β-diversity analysis indicated that the two dietary treatments were associated with distinct bacterial communities. The AF diet had a significantly higher abundance of Bacteroidota and a lower abundance of Actinomycetota, Acidobacteriota, and Chloroflexota compared to the NF group. In addition, Bacteroidota was the biomarker in the gut of mandarin fish from the AF treatment, while Acidobacteriota was distinguished in the NF treatments. Additionally, the increased abundance of Bacteroidota in the AF diet group contributed to the improved fermentation and nutrient assimilation, as supported by the metabolic functional prediction and transcriptome verification. Overall, the present work used the mandarin fish as a vertebrate model to uncover the effects of habitual dietary changes on the evolution of the host microbiota, which may provide potential insights for the substitution of natural foods by processed foods in mammals., Competing Interests: The authors declare that they have no competing interests., (© 2024 Li et al.)

Biochar, which including pyrochar (PBC) and hydrochar (HBC), has been tested as a soil enhancer to improve saline soils. However, the effects of PBC and HBC application on ammonia (NH 3 ) volatilization and dissolved organic matter (DOM) in saline paddy soils are poorly understood. In this research, marsh moss-derived PBC and HBC biochar types were applied to paddy saline soils at 0.5 % (w/w) and 1.5 % (w/w) rates to assess their impact on soil NH 3 volatilization and DOM using a soil column experiment. The results revealed that soil NH 3 volatilization significantly increased by 56.1 % in the treatment with 1.5 % (w/w) HBC compared to the control without PBC or HBC. Conversely, PBC and the lower application rate of HBC led to decrease in NH 3 volatilization ranging from 2.4 % to 12.1 %. Floodwater EC is a dominant factor in NH 3 emission. Furthermore, the fluorescence intensities of the four fractions (all humic substances) were found to be significantly higher in the 1.5 % (w/w) HBC treatment applied compared to the other treatments, as indicated by parallel factor analysis modeling. This study highlights the potential for soil NH 3 losses and DOM leaching in saline paddy soils due to the high application rate of HBC. These findings offer valuable insights into the effects of PBC and HBC on rice paddy saline soil ecosystems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Diets with high carbohydrate (HC) was reported to have influence on appetite and intermediary metabolism in fish. To illustrate whether betaine could improve appetite and glucose-lipid metabolism in aquatic animals, mandarin fish ( Siniperca chuatsi ) were fed with the HC diets with or without betaine for 8 weeks. The results suggested that betaine enhanced feed intake by regulating the hypothalamic appetite genes. The HC diet-induced downregulation of AMPK and appetite genes was also positively correlated with the decreased autophagy genes, suggesting a possible mechanism that AMPK/mTOR signaling might regulate appetite through autophagy. The HC diet remarkably elevated transcriptional levels of genes related to lipogenesis, while betaine alleviated the HC-induced hepatic lipid deposition. Additionally, betaine supplementation tended to store the energy storage as hepatic glycogen. Our findings proposed the possible mechanism for appetite regulation through autophagy via AMPK/mTOR, and demonstrated the feasibility of betaine as an aquafeed additive to regulate appetite and intermediary metabolism in fish., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

MiRNAs are edited or modified in multiple ways during their biogenesis pathways. It was reported that miRNA editing was deregulated in tumors, suggesting the potential value of miRNA editing in cancer classification. Here we extracted three types of miRNA features from 395 LUAD and control samples, including the abundances of original miRNAs, the abundances of edited miRNAs, and the editing levels of miRNA editing sites. Our results show that eight classification algorithms selected generally had better performances on combined features than on the abundances of miRNAs or editing features of miRNAs alone. One feature selection algorithm, i.e., the DFL algorithm, selected only three features, i.e., the frequencies of hsa-miR-135b-5p, hsa-miR-210-3p and hsa-mir-182&#95;48u (an edited miRNA), from 316 training samples. Seven classification algorithms achieved 100% accuracies on these three features for 79 independent testing samples. These results indicate that the additional information of miRNA editing is useful in improving the classification of LUAD samples., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Phased secondary small interfering RNAs (phasiRNAs) in plants play important roles in regulating genome stability, plant development and stress adaption. Camellia sinensis var. assamica has immense economic, medicinal and cultural significance. However, there are still no studies of phasiRNAs and their putative functions in this valuable plant. We identified 476 and 43 PHAS loci which generated 4290 twenty one nucleotide (nt) and 264 twenty four nt phasiRNAs, respectively. Moreover, the analysis of degradome revealed more than 35000 potential targets for these phasiRNAs. We identified several conserved 21 nt phasiRNA generation pathways in tea plant, including miR390 → TAS3, miR482/miR2118 → NB-LRR, miR393 → F-box, miR828 → MYB/TAS4, and miR7122 → PPR in this study. Furthermore, we found that some transposase and plant mobile domain genes could generate phasiRNAs. Our results show that phasiRNAs target genes in the same family in cis - or trans -manners, and different members of the same gene family may generate the same phasiRNAs. The phasiRNAs, generated by transposase and plant mobile domain genes, and their targets, suggest that phasiRNAs may be involved in the inhibition of transposable elements in tea plant. To summarize, these results provide a comprehensive view of phasiRNAs in Camellia sinensis var. assamica ., (© The Author(s) 2023. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)

Polycyclic aromatic hydrocarbons (PAHs) residues in fish, shrimp and shellfish have attracted attention because they are major species in the aquatic food chain and an important food source for humans. These organisms have various feeding habits and different living environments, and through the food chain, they can directly or indirectly connect particulate organic matter and human consumption. However, little attention has been paid to the bioaccumulation of PAHs in aquatic organism groups representing varied conditions and feeding habits in the food chain. In this study, 17 species of aquatic organisms, comprising fish, shrimp, and shellfish, were captured from 15 locations distributed within the river network of the Pearl River Delta. The concentration of 16 PAHs was measured in the aquatic organisms. The sum of the 16 measured PAHs ranged from 57.39 to 696.07 ng/g, dry weight, while phenanthrene had the highest individual content. The linear mixed effect model was applied to estimate the random effects of PAH accumulation in aquatic organisms. The result showed that the contributed proportion of variance to feeding habits (58.1 %) was higher than that of geographic distribution (11.8 %). In addition, one-way analysis of variance (ANOVA) demonstrated that the concentrations of PAHs depended on the water layer inhabited by the organism and its species status. Specifically, shellfish and carnivorous bottom-dwelling fish showed significantly higher levels than other aquatic organisms., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

To investigate the impact of betaine on high-carbohydrate-diet-induced oxidative stress and endoplasmic reticulum (ER) stress, mandarin fish ( Siniperca chuatsi ) (23.73 ± 0.05 g) were fed with control (NC), betaine (BET), high carbohydrate (HC), and high carbohydrate + betaine (HC + BET) diets for 8 weeks. The results showed that betaine significantly promoted the growth of mandarin fish irrespective of the dietary carbohydrate levels. The HC diet induced oxidative stress, as evidenced by significantly elevated MDA levels. The HC diet significantly stimulated the mRNA levels of genes involved in ER stress ( ire1 , perk , atf6 , xbp1 , eif2α , atf4 , chop ), autophagy ( ulk1 , becn1 , lc3b ), and apoptosis ( bax ). However, betaine mitigated HC-diet-induced oxidative stress by modulating antioxidant enzymes and alleviated ER stress by regulating the mRNA of genes in the PERK-eIF2a-ATF4 pathway. Additionally, betaine significantly reduced the mRNA levels of becn1 and bax , along with the apoptosis rate, indicating a mitigating effect on autophagy and apoptosis. Overall, dietary betaine improved growth, attenuated HC-diet-induced oxidative stress and ER stress, and ultimately alleviated apoptosis in mandarin fish. These findings provide evidence for the use of betaine in aquafeeds to counter disruptive effects due to diets containing high carbohydrate levels.

Clear cell renal cell carcinoma (ccRCC) is a malignant tumor originating from the renal tubular epithelium. Although the microRNAs (miRNAs) transcriptome of ccRCC has been extensively studied, the role of miRNAs editing in ccRCC is largely unknown. By analyzing small RNA sequencing profiles of renal tissues of 154 ccRCC patients and 22 normal controls, we identified 1025 miRNA editing sites from 246 pre-miRNAs. There were 122 editing events with significantly different editing levels in ccRCC compared to normal samples, which include two A-to-I editing events in the seed regions of hsa-mir-376a-3p and hsa-mir-376c-3p, respectively, and one C-to-U editing event in the seed region of hsa-mir-29c-3p. After comparing the targets of the original and edited miRNAs, we found that hsa-mir-376a-1&#95;49g, hsa-mir-376c&#95;48g and hsa-mir-29c&#95;59u had many new targets, respectively. Many of these new targets were deregulated in ccRCC, which might be related to the different editing levels of hsa-mir-376a-3p, hsa-mir-376c-3p, hsa-mir-29c-3p in ccRCC compared to normal controls. Our study sheds new light on miRNA editing events and their potential biological functions in ccRCC., (© 2023. Springer Nature Limited.)

The accumulation of pyrethroid insecticides in aquatic food webs has attracted increased research attention. Fish are key species in aquatic food webs, directly connecting invertebrates and human consumption. However, little is known about the bioaccumulation of pyrethroids in wild fish species. In this study, 19 species of wild fish were collected from 11 sites in the Pearl River, China, and the levels of seven pyrethroids in the fish were determined. Linear mixed-effects models were applied to estimate the means of pyrethroid concentrations, in which sample site and fish species were set as random effects. The concentrations of Σ 7 pyrethroids in fish ranged from 4.99 to 50.82 ng/g. Permethrin and bifenthrin were present at the highest concentration (8.89 ± 1.47 ng/g) and frequency (100%) in fish muscle, respectively. The composition patterns of pyrethroids varied in fish organs. Fish species contributed a higher proportion of the variance than geographic distribution (28.6% vs. 26.4%). The pyrethroids in carnivorous fish (23.5 ± 2.9 ng/g) were significantly higher than in omnivorous (14.6 ± 1.9 ng/g) and phytophagous fish (16.0 ± 4.7 ng/g). To our knowledge, this is the first report examining the effect of feeding habits on pyrethroid bioaccumulation in wild fish. The results can provide evidence for the risk of pyrethroid pollution in aquatic ecosystems., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The agricultural ecological system is an important part of the Yellow River Delta (YRD); however, soil reclamation may trigger environmental concerns about nitrate leaching and NH 3 volatilization in this area. To assess nitrogen losses during soil reclamation, a two-year field experiment was conducted with plastic film mulch, which is an effective way to alleviate water-salt stress. The Hydrus-2D software package was used to calculate nitrogen transport, transformation and losses. The results showed that nitrogen (N) retention in the soil varied during the two growing seasons, because soil water, salinity and climatic conditions acted together on nitrogen transport and transformation. Soil salinity promoted NH 3 volatilization, and the proportions of ammonia volatilization were 22.78 percent and 19.50 percent of the N input in 2018 and 2019, respectively, because urea hydrolysis, nitrification and soil NH 4 + -N adsorption capacity were limited by soil salt. NO 3 - -N leaching was controlled by soil water infiltration, climatic conditions and groundwater level. NO 3 - -N leaching was 43.84 percent and 32.89 percent of the nitrogen input in 2018 and 2019, respectively; the difference was mainly caused by the different distribution of rainfall during the growing season; thus, soil water infiltration increased under heavy rainfall because it broke the barrier formed by the plough pan. This study indicates that there is a risk of nitrogen pollution during soil reclamation. In addition, Hydrus-2D has considerable potential to calculate nitrogen losses under the effect of plastic film mulch in this area., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Background: With the rising incidences stroke, the Post-Stroke Urinary Incontinence (PSUI) has become one of the common clinical sequelae. PSUI not only lowers the quality of life of patients, but also impacts tremendously to mental health. As a treasure of Chinese medicine, acupuncture and its related therapies have been widely accepted in clinical treatment of PSUI. Recently, there have been many clinical studies on the treatment of PSUI with acupuncture and related therapies, but the best way to treat PSUI is controversial. Therefore, the purpose of this paper is to provide an optimal ranking regarding acupuncture and its related therapies for PSUI., Methods: The five domestic and foreign databases including PubMed, Embase, Cochrane Library, China National Knowledge Infrastructure, Wanfang Database will be systematically searched. The time range of the literature search is from the date of establishment to August 31, 2020. The main evaluation outcome was the number of patients after treatment, and the frequency of urinary incontinence. The secondary evaluation outcome was International Consultation on Incontinence Questionnaire-Short Form (ICIQ-SF), Barthel Activities of Daily Living Index (Barthel ADL Index) and the incidence rate of adverse events. The methodological quality of the article will evaluated by Cochrane Collaboration's Tool and the quality of evidence will evaluated through Grading of Recommendations Assessment, Development and Evaluation (GRADE) instrument. The Network Meta-Analysis (NMA) will be completed using Stata statistical software., Results: The final results of this study will be published in a peer-reviewed journal., Conclusion: This network meta-analysis will compare the efficacy and safety of different acupuncture therapies in the treatment of PSUI and summarize the best treatment options, which will help patients and doctors to choose effective acupuncture methods in time.

High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42-0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement.

Aging is a risk factor for cardiovascular disease, and there is no effective therapeutic approach to alleviate this condition. NF- κ B and TNF- α have been implicated in the activation of the aging process, but the signaling molecules responsible for the inactivation of NF- κ B and TNF- α remain unknown. Exosomes have been reported to improve heart functions by releasing miRNA. Recent studies suggest that lncRNAs are more tissue-specific and developmental stage-specific compared to miRNA. However, the role of lncRNA in exosome-mediated cardiac repair has not been explored. In the present study, we focused on metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), which is an lncRNA associated with cell senescence. We discovered that human umbilical cord mesenchymal stem cell- (UMSC-) derived exosomes prevent aging-induced cardiac dysfunction. Silencer RNA against lncRNA MALAT1 blocked the beneficial effects of exosomes. In summary, we discovered that UMSC-derived exosomes prevent aging-induced cardiac dysfunction by releasing novel lncRNA MALAT1, which in turn inhibits the NF- κ B/TNF- α signaling pathway. These findings will lead to the development of therapies that delay aging and progression of age-related diseases.

Highly efficient biosynthesis of the commercially valuable carotenoid astaxanthin by microbial cells is an attractive alternative to chemical synthesis and microalgae extraction. With the goal of enhancing heterologous astaxanthin production in Saccharomyces cerevisiae, metabolic engineering and protein engineering were integrated to improve both the expression and activity of rate-limiting enzymes. Firstly, to increase the supply of β-carotene as a key precursor for astaxanthin, a positive mutant of GGPP synthase (CrtE03M) was overexpressed together with three other rate-limiting enzymes tHMG1, CrtI and CrtYB. Subsequently, to accelerate the conversion of β-carotene to astaxanthin, a color screening system was developed and adopted for directed evolution of β-carotene ketolase (OBKT), generating a triple mutant OBKTM (H165R/V264D/F298Y) with 2.4-fold improved activity. After adjusting copy numbers of the above-mentioned rate-limiting enzymes to further balance the metabolic flux, a diploid strain YastD-01 was generated by mating two astaxanthin-producing haploid strains carrying the same carotenogenic pathway. Finally, further overexpression of OCrtZ and OBKTM in YastD-01 resulted in accumulation of 8.10mg/g DCW (47.18mg/l) of (3S, 3'S)-astaxanthin in shake-flask cultures. This combinatorial strategy might be also applicable for alleviation of metabolic bottleneck in biosynthesis of other value-added products, especially colored metabolites., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Fine-tuning the expression level of an engineered pathway is crucial for the metabolic engineering of a host toward a desired phenotype. However, most engineered hosts suffer from nonfunctional protein expression, metabolic imbalance, cellular burden or toxicity from intermediates when an engineered pathway is first introduced, which can decrease production of the desired product. To circumvent these obstacles, we developed a self-regulation system utilizing the trc/tac promoter, LacI(q) protein and ribosomal binding sites (RBS). With the purpose of improving coenzyme Q10 (CoQ10 ) production by increasing the decaprenyl diphosphate supplement, enzymes DXS, DXR, IDI, and IspD were constitutively overexpressed under the control of the trc promoter in Rhodobacter sphaeroides. Then, a self-regulation system combining a set of RBSs for adjusting the expression of the LacI(q) protein was applied to tune the expression of the four genes, resulting in improved CoQ10 production. Finally, another copy of the tac promoter with the UbiG gene (involved in the ubiquinone pathway of CoQ10 biosynthesis) was introduced into the engineered pathway. By optimizing the expression level of both the upstream and downstream pathway, CoQ10 production in the mutants was improved up to 93.34 mg/L (7.16 mg/g DCW), about twofold of the wild-type (48.25 mg/L, 3.24 mg/g DCW)., (© 2013 Wiley Periodicals, Inc.)