Transcriptome analysis revealed the existence of family-specific regulation of growth traits in grass carp.

The grass carp (Ctenopharyngodon idella) is the world's most prolific freshwater fish. Little is known, however, about the functional genes and genetic regulatory networks that govern its growth traits. We created three grass carp families in this study by using two grass carp parents with fast-growing offspring and two grass carp parents with slow-growing offspring, namely the fast-growing × fast-growing family (FF), the slow-growing × slow-growing family (SS), and the fast-growing × slow-growing family (FS). Under the satiation and starvation feeding modes, the average body weight of these families' offspring exhibited a consistent ordering (FF > FS > SS). The transcriptomes of grass carp whole brain and hepatopancreas were then acquired for each family, and it was discovered that the number of differentially expressed genes (DEGs) in the different organs demonstrated family specificity. DEGs were mostly identified in the hepatopancreas of FF and the whole brain of SS, but they were more evenly distributed in FS. There were 14 DEGs that were found in all three families, including three that were negatively correlated in hepatopancreas (ahsg2, lect2) or in brain (drd5), and 11 that were positively connected in hepatopancreas (sycn, pabpc4, zgc:112294, cel, endou, ela2, prss3, zbtb41, ela3) or in brain (fabp7, endod1). The deletion of ahsg2 boosted the growth rate only in certain zebrafish, suggesting that the growth-promoting effects of ahsg2 varies among individuals. Furthermore, we examined the SNP in each family and conducted preliminary research on the probable genetic pathways of family-specific control of growth traits. The family specificity of the growth regulation mechanism of grass carp at the transcriptional level was revealed for the first time in this study, and it was discovered that growth differences among individuals in the FF family were primarily due to differences in nutrient metabolism, whereas growth differences among individuals in the SS family may be primarily due to differences in foraging ability caused by differences in brain development. This research adds to our understanding of the genetic regulatory mechanism of grass carp growth.

A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs.

High-throughput RNA sequencing unveiled the complexity of transcriptome and significantly increased the records of long noncoding RNAs (lncRNAs), which were reported to participate in a variety of biological processes. Identification of lncRNAs is a key step in lncRNA analysis, and a bunch of bioinformatics tools have been developed for this purpose in recent years. While these tools allow us to identify lncRNA more efficiently and accurately, they may produce inconsistent results, making selection a confusing issue. We compared the performance of 41 analysis models based on 14 software packages and different data sets, including high-quality data and low-quality data from 33 species. In addition, computational efficiency, robustness, and joint prediction of the models were explored. As a practical guidance, key points for lncRNA identification under different situations were summarized. In this investigation, no one of these models could be superior to others under all test conditions. The performance of a model relied to a great extent on the source of transcripts and the quality of assemblies. As general references, FEELnc_all_cl, CPC, and CPAT_mouse work well in most species while COME, CNCI, and lncScore are good choices for model organisms. Since these tools are sensitive to different factors such as the species involved and the quality of assembly, researchers must carefully select the appropriate tool based on the actual data. Alternatively, our test suggests that joint prediction could behave better than any single model if proper models were chosen. All scripts/data used in this research can be accessed at http://bioinfo.ihb.ac.cn/elit.

Stannate-Based Materials as Anodes in Lithium-Ion and Sodium-Ion Batteries: A Review.

Binary metal oxide stannate (M2SnO4; M = Zn, Mn, Co, etc.) structures, with their high theoretical capacity, superior lithium storage mechanism and suitable operating voltage, as well as their dual suitability for lithium-ion batteries (LIBs) and sodium-ion batteries (SIBs), are strong candidates for next-generation anode materials. However, the capacity deterioration caused by the severe volume expansion problem during the insertion/extraction of lithium or sodium ions during cycling of M2SnO4-based anode materials is difficult to avoid, which greatly affects their practical applications. Strategies often employed by researchers to address this problem include nanosizing the material size, designing suitable structures, doping with carbon materials and heteroatoms, metal-organic framework (MOF) derivation and constructing heterostructures. In this paper, the advantages and issues of M2SnO4-based materials are analyzed, and the strategies to solve the issues are discussed in order to promote the theoretical work and practical application of M2SnO4-based anode materials.

Maternal serum CFHR4 protein as a potential non-invasive marker of ventricular septal defects in offspring: evidence from a comparative proteomics study.

BACKGROUND: Despite advances in diagnosis of congenital heart defects, there is no non-invasive biomarker clinically available for the early detection of fetal ventricular septal defects (VSD). METHODS: This study was to profile differentially expressed proteins (DEP) in the first trimester maternal plasma samples that were collected in the 12th-14th week of gestation and identify potential biomarkers for VSD. Maternal plasma samples of ten case-control pairs of women (who had given birth to an isolated VSD infant or not) were selected from a birth cohort biospecimen bank for identifying DEPs by using high-performance liquid chromatography-tandem mass spectrometry-based comparative proteomics. RESULTS: There were 35 proteins with significantly different levels between cases and controls, including 9 upregulated and 26 downregulated proteins. With Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway enrichment, and protein-protein interaction analyses, most of the DEPs were clustered in pathways related to B cell-mediated immune responses, complement activation, and phagocytosis. Three DEPs were validated using enzyme-linked immunosorbent assay in another set of samples consisting of 31 cases and 33 controls. And CFHR4, a key regulator in complement cascades, was found to be significantly upregulated in cases as compared to controls. CONCLUSIONS: Subsequent logistic regression and receiver operating characteristic analysis suggested maternal serum CFHR4 as a promising biomarker of fetal VSD. Further studies are warranted to verify the findings.

Comprehensive analysis of hub mRNA, lncRNA and miRNA, and associated ceRNA networks implicated in grass carp (Ctenopharyngodon idella) growth traits.

Grass carp (Ctenopharyngodon idella) is the most productive freshwater aquaculture fish in worldwide. However, the molecular mechanism of its growth traits has not been fully elucidated. Whole transcriptome analysis of the brain and hepatopancreas of 29 six-month-old grass carp with different growth rates was performed. Weighted gene co-expression network analysis (WGCNA) was used to construct a weighted gene co-expression network of mRNA, miRNA and lncRNA separately. A total of 35 hub mRNAs, 47 hub lncRNAs and 33 hub miRNAs were identified from the brain, 37 hub mRNAs, 110 hub lncRNAs and 36 hub miRNAs were identified from the hepatopancreas. The ceRNA networks in the brain and hepatopancreas were involved in brain development and nutrient metabolism, respectively. Overall, this is the first investigation of the growth-related transcriptomic characteristics in the brain and hepatopancreas of grass carp, thus will help us to further explore the molecular mechanism of grass carp growth rate.

Dynamic Transcriptional Landscape of Grass Carp (Ctenopharyngodon idella) Reveals Key Transcriptional Features Involved in Fish Development.

A high-quality baseline transcriptome is a valuable resource for developmental research as well as a useful reference for other studies. We gathered 41 samples representing 11 tissues/organs from 22 important developmental time points within 197 days of fertilization of grass carp eggs in order to systematically examine the role of lncRNAs and alternative splicing in fish development. We created a high-quality grass carp baseline transcriptome with a completeness of up to 93.98 percent by combining strand-specific RNA sequencing and single-molecule real-time RNA sequencing technologies, and we obtained temporal expression profiles of 33,055 genes and 77,582 transcripts during development and tissue differentiation. A family of short interspersed elements was preferentially expressed at the early stage of zygotic activation in grass carp, and its possible regulatory components were discovered through analysis. Additionally, after thoroughly analyzing alternative splicing events, we discovered that retained intron (RI) alternative splicing events change significantly in both zygotic activation and tissue differentiation. During zygotic activation, we also revealed the precise regulatory characteristics of the underlying functional RI events.

Edwardsiella piscicida type III protein EseJ suppresses apoptosis through down regulating type 1 fimbriae, which stimulate the cleavage of caspase-8.

The type III secretion system effector EseJ plays a regulatory role inside bacteria. It suppresses the adherence of Edwardsiella piscicida (E. piscicida) to host epithelial cells by down regulating type 1 fimbriae. In this study, we observed that more macrophages infected with ΔeseJ strain of E. piscicida detached as compared with those infected with the wild-type (WT) strain. Terminal deoxynucleotidyl transferase dUTP nick-end labelling (TUNEL) staining and cleaved caspase-3 examination revealed that the detachment is due to increased apoptosis, suggesting that EseJ suppresses macrophage apoptosis. However, apoptosis inhibition by EseJ is not relative to a type III secretion system (T3SS) and is not related to EseJ's translocation. Since EseJ negatively regulates type 1 fimbriae, murine J774A.1 cells were infected with ΔeseJΔfimA or ΔeseJΔfimH strains. It was demonstrated that ΔeseJ stimulates macrophage apoptosis through type 1 fimbriae. Moreover, we found that infecting J774A.1 cells with the ΔeseJ strain increased levels of cleaved caspase-8, caspase-9, and caspase-3, demonstrating that EseJ inhibits apoptosis through either an extrinsic or a combination of extrinsic and intrinsic pathways. Pre-treatment of macrophages with caspase-8 inhibitor prior to infection with the ΔeseJ strain decreased the levels of cleaved caspase-8, caspase-9, and caspase-3, indicating that the ΔeseJ strain stimulates apoptosis, mainly through an extrinsic pathway by up regulating type 1 fimbriae. Zebrafish larvae or blue gourami fish infected with the ΔeseJ strain consistently exhibited higher apoptosis than those infected with the E. piscicida WT strain or ΔeseJΔfimA strain. Taken together, we revealed that the T3SS protein EseJ of E. piscicida inhibits host apoptosis, mainly through an extrinsic pathway by down regulating type 1 fimbriae.

Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus).

BACKGROUND: Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. A draft genome for grass carp has already been published in 2015. However, there is still a requirement for a suitable genetic linkage map to arrange scaffolds on chromosomal frameworks. QTL analysis is a powerful tool to detect key locations for quantitative traits, especially in aquaculture. There no growth related QTLs of grass carp have been published yet. Even the growth trait is one of the focuses in grass carp culture. RESULTS: In this study, a pair of distantly related parent grass carps and their 100 six-month-old full-sib offspring were used to construct a high-density genetic map with 6429 single nucleotide polymorphisms (SNPs) by 2b-RAD technology. The total length of the consensus map is 5553.43 cM with the average marker interval of 1.92 cM. The map has a good collinearity with both the grass carp draft genome and the zebrafish genome, and it assembled 89.91% of the draft genome to a chromosomal level. Additionally, according to the growth-related traits of progenies, 30 quantitative trait loci (QTLs), including 7 for body weight, 9 for body length, 5 for body height and 9 for total length, were identified in 16 locations on 5 linkage groups. The phenotypic variance explained for these QTLs varies from 13.4 to 21.6%. Finally, 17 genes located in these regions were considered to be growth-related because they either had functional mutations predicted from the resequencing data of the parents. CONCLUSION: A high density genetic linkage map of grass carp was built and it assembled the draft genome to a chromosomal level. Thirty growth related QTLs were detected. After the cross analysis of Parents resequencing data, 17 candidate genes were obtained for further researches.

Glutathione peroxidase 5 deficiency induces lipid metabolism regulated by reactive oxygen species in Chlamydomonas reinhardtii.

BACKGROUND: Reactive oxygen species (ROS) are generated incidentally during natural metabolism process of aerobic photosynthetic organisms which could be either harmful for cellular components. How ROS regulated lipid metabolism and the transcriptomes of stressed cells respond to ROS in aerobic photosynthetic organisms are unclear. Glutathione peroxidases (GPXs) detoxify hydrogen peroxide or organic hydroperoxides, which are important enzymes of the antioxidant system. So the function of GPXs matters the cellular redox state. How the lipid metabolism respond to the GPXs deficiency remains to be explored. METHODS: In this study, we employed a Chlamydomonas reinhardtii gpx5 knockout mutant to examine the effects of ROS on lipid metabolism. The redox state and lipid content of the parental strain CC4348 and the gpx5 mutant were detected. Besides, the transcriptomes of CC4348 and the gpx5 mutant were sequenced before and after treatment with nitrogen-free medium to obtain genome wide respond. Then we performed the functional annotation, classification and enrichment analysis based on KEGG database for the differentially expressed genes (DEGs) before and after nitrogen deprivation of CC4348 and the gpx5 mutant. RESULTS: In the CC4348 cells, the lipid accumulated accompanying with increasing ROS level after treatment with nitrogen-free media. However, in the gpx5 mutant, the ROS level is much higher than that in the parental strain CC4348, unexpectedly with reduced lipid accumulation. By comparing the transcriptomes of CC4348 and gpx5 mutant, we found that both CC4348 and gpx5 mutant cells displayed upregulation of transcripts related to protein, nucleic acid, carbon metabolism and chlorophyll biosynthesis, but more proportion of genes related to lipid metabolism were up-regulated in CC4348 than that in the gpx5 mutant. CONCLUSION: In CC4348, lipid metabolism was up-regulated with increasing ROS level. But in the gpx5 mutant, Lipid accumulation was less with higher ROS level, which was due to the inhibited lipid biosynthesis. Therefore, ROS provides dual-directional regulation of lipid metabolism induced by GPX5 in Chlamydomonas.

The Edwardsiella piscicida Type III Effector EseJ Suppresses Expression of Type 1 Fimbriae, Leading to Decreased Bacterial Adherence to Host Cells.

The type III secretion system (T3SS) of Edwardsiella piscicida plays a crucial role in its pathogenesis. Our previous study indicated that the T3SS effector protein EseJ inhibits the bacterium's adhesion to epithelioma papillosum cyprini (EPC) cells, while the mechanism of the inhibition remains elusive. In this study, we revealed that EseJ negatively regulates the fimA gene, as demonstrated by comparative transcription analysis of ΔeseJ and wild-type (WT) strains. As well, the dramatically increased production of FimA was detected in the absence of EseJ compared to that by the WT strain. The adherence of the ΔeseJ strain decreased far below that of the WT strain in the absence of FimA, demonstrating that FimA plays a pivotal role in the hyperadhesion of the ΔeseJ strain. Adherence analysis with a strain with truncated eseJ demonstrated that the C-terminal region of EseJ (Gly1191 to Ile1359) is necessary to inhibit the transcription of the type 1 fimbrial operon. Binding between the EseJ fragment from amino acid residues 1191 to 1359 and the DNA fragment upstream of fimA was not detected, indicating that EseJ might indirectly regulate the type 1 fimbrial operon. Our study reveals that EseJ controls E. piscicida adherence to EPC cells by negatively regulating the type 1 fimbrial operon.

RpoN (σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain.

Some bacteria are capable of forming flocs, in which bacterial cells become self-flocculated by secreted extracellular polysaccharides and other biopolymers. The floc-forming bacteria play a central role in activated sludge, which has been widely utilized for the treatment of municipal sewage and industrial wastewater. Here, we use a floc-forming bacterium, Aquincolatertiaricarbonis RN12, as a model to explore the biosynthesis of extracellular polysaccharides and the regulation of floc formation. A large gene cluster for exopolysaccharide biosynthesis and a gene encoding the alternative sigma factor RpoN1, one of the four paralogues, have been identified in floc formation-deficient mutants generated by transposon mutagenesis, and the gene functions have been further confirmed by genetic complementation analyses. Interestingly, the biosynthesis of exopolysaccharides remained in the rpoN1-disrupted flocculation-defective mutants, but most of the exopolysaccharides were secreted and released rather than bound to the cells. Furthermore, the expression of exopolysaccharide biosynthesis genes seemed not to be regulated by RpoN1. Taken together, our results indicate that RpoN1 may play a role in regulating the expression of a certain gene(s) involved in the self-flocculation of bacterial cells but not in the biosynthesis and secretion of exopolysaccharides required for floc formation.IMPORTANCE Floc formation confers bacterial resistance to predation of protozoa and plays a central role in the widely used activated sludge process. In this study, we not only identified a large gene cluster for biosynthesis of extracellular polysaccharides but also identified four rpoN paralogues, one of which (rpoN1) is required for floc formation in A. tertiaricarbonis RN12. In addition, this RpoN sigma factor regulates the transcription of genes involved in biofilm formation and swarming motility, as previously shown in other bacteria. However, this RpoN paralogue is not required for the biosynthesis of exopolysaccharides, which are released and dissolved into culture broth by the rpoN1 mutant rather than remaining tightly bound to cells, as observed during the flocculation of the wild-type strain. These results indicate that floc formation is a regulated complex process, and other yet-to-be identified RpoN1-dependent factors are involved in self-flocculation of bacterial cells via exopolysaccharides and/or other biopolymers.

Application of Dynamic Contrast-Enhanced Ultrasound in Evaluation the Activity of Crohn's Disease.

BACKGROUND AND OBJECTIVE: The dynamic assessment of disease activity during the follow-up of patients with Crohn's disease (CD) remains a significant challenge. In this study, we aimed to identify the role of dynamic contrast-enhanced ultrasound (DCE-US) in the evaluation of activity of CD. METHODS: In the retrospective study, patients diagnosed with CD in our hospital were included. All the diagnoses were confirmed by clinical symptoms and ileocolonoscopical results. All patients underwent intestinal ultrasound and contrast-enhanced ultrasound (CEUS) examinations within 1 week of the ileocolonoscopy examinations. Acuson Sequoia (Siemens Healthineers, Mountain View, CA, USA) and Resona R9 Elite (Mindray Medical Systems, China) with curved array and Line array transducers were used. The CEUS examination was performed with SonoVue (Bracco SpA, Milan, Italy). DCE-US analysis was performed by UltraOffice (version: 0.3-2010, Mindray Medical Systems, China) software. Two regions of interest (ROIs) were set in the anterior section of the infected bowel wall and its surrounding normal bowel wall 2 cm distant from the inflamed area. Time-intensity curves (TICs) were generated and quantitative perfusion parameters were obtained after curve fittings. The Simple Endoscopic Score for Crohn's disease (SES-CD) was regarded as the reference standard to evaluate the activity of CD. The receiver operating characteristic curve (ROC) analyses were used to determine the diagnostic efficiency of DCE-US quantitative parameters. RESULTS: From March 2023 to November 2023, 52 CD patients were included. According to SES-CD score, all patients were divided into active group with the SES-CD score > 5 (n = 39) and inactive group SES-CD score < 5 (n = 13). Most of the active CD patients showed bowel wall thickness (BWT) > 4.2 mm (97.4%, 38/39) or mesenteric fat hypertrophy (MFH) on intestinal ultrasound (US) scan (69.2%, 27/39). Color Doppler signal of the bowel wall mostly showed spotty or short striped blood flow signal in active CD patients (56.4%, 22/39). According to CEUS enhancement patterns, most active CD patients showed a complete hyperenhancement of the entire intestinal wall (61.5%, 24/39). The TICs of active CD showed an earlier enhancement, higher peak intensity, and faster decline. Among all CEUS quantitative parameters, amplitude-derived parameters peak enhancement (PE), wash-in area under the curve (WiAUC), wash-in rate (WiR), wash-in perfusion index (WiPI), and wash-out rate (WoR) were significantly higher in active CD than in inactive CD (p < 0.05). The combined AUROC of intestinal ultrasound features and DCE-US quantitative perfusion parameters in the diagnosis of active CD was 0.987, with 97.4% sensitivity, 100% specificity, and 98.1% accuracy. CONCLUSIONS: DCE-US with quantitative perfusion parameters is a potential useful noninvasive imaging method to evaluate the activity of Crohn's disease.

FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization.

With the rapid expansion of transcriptome studies in many fishes, a great number of RNA-seq data have been published, allowing for a more systematic understanding of the general profiles and details of gene expression in fish. FishGET is dedicated to gathering and curating fish RNA-seq data to discover more new RNAs, including mRNA and lncRNA, thereby getting a more complete reference transcriptome and providing more comprehensive and accurate transcriptome annotations. We obtained a total of 1362 RNA-seq paired-end data of 8 fishes from 97 different studies, and then we performed transcript assembly, meta-assembly, weighted gene co-expression network analysis (WGCNA), functional annotations, neighbor location annotation, lncRNA type annotation, homology annotation. To promote research into fish genes at the transcriptional level, we developed a user-friendly web interface that allows users to view all information and makes use of multiple types of dynamic interactive visualization services.

Potential risk of eutrophication in the deepest lake of Southwest China: Insights from phosphorus enrichment in bottom water.

Large deep lakes in plateau regions provide crucial ecosystem services but are susceptible to eutrophication due to their long water residence time. To date, the water quality of deep lakes has not received as much attention as that of shallow lakes owing to logistical challenges. This study investigated the seasonal variation and vertical distribution of phosphorus and related environmental variables in a large deep lake in the Yunnan Plateau, China (Fuxian Lake). Generally, the concentrations of total phosphorus (TP, R2 = 0.862), total dissolved phosphorus (TDP, R2 = 0.922), and dissolved inorganic phosphorus (DIP, R2 = 0.889) exhibited a linear increase with the greater water depth, whereas the pH and dissolved oxygen (DO) showed decreasing trends. The TP, TDP, and DIP values were 0.012, 0.006, and 0.004 mg/L, respectively, in surface waters (0.5 m depth), and increased to 0.074, 0.065, and 0.062 mg/L, respectively, at 140.0 m depth. The averaged over ordering method demonstrated that DO and air temperature accounted for a higher proportion of the explained variance of TP, TDP, and DIP in the shallow water layer (0.5-20.0 m). In contrast, DO and pH accounted for a higher proportion of the explained variance of TP, TDP, and DIP in deeper water layers (40.0-150.0 m). As a warm monomictic lake, the higher observed phosphorus concentrations in deeper water and sediment potentially pose a risk of future eutrophication in the Fuxian Lake. Our findings demonstrate that more efficient technical and management measures should be taken to reduce the external phosphorus load to Fuxian Lake, so that the load to and from the sediment will decrease eventually.

Disulfiram enhances cisplatin cytotoxicity by forming a novel platinum chelate Pt(DDTC)3.

Despite the use of targeted therapy in non-small cell lung cancer (NSCLC) patients, cisplatin (DDP)-based chemotherapy is still the main option. However, DDP resistance is the major factor contributing to the failure of chemotherapy. In this study, we tried to screen DDP sensitizers from an FDA-approved drug library containing 1374 small-molecule drugs to overcome DDP resistance in NSCLC. As a result, disulfiram (DSF) was identified as a DDP sensitizer: DSF and DDP had synergistic anti-NSCLC effects, which are mainly reflected in inhibiting tumor cell proliferation, plate colony formation and 3D spheroidogenesis and inducing apoptosis in vitro, as well as the growth of NSCLC xenografts in mice. Although DSF has recently been reported to promote the antitumor effect of DDP by inhibiting ALDH activity or modulating some important factors or pathways, unexpectedly, we found that DSF reacted with DDP to form a new platinum chelate, Pt(DDTC)3+, which might be one of the important mechanisms for their synergistic effect. Moreover, Pt(DDTC)3+ has a stronger anti-NSCLC effect than DDP, and its antitumor activity is broad-spectrum. These findings reveal a novel mechanism underlying the synergistic antitumor effect of DDP and DSF, and provide a drug candidate or a lead compound for the development of a new antitumor drug.

Biodegradable nanoparticles of mPEG-PLGA-PLL triblock copolymers as novel non-viral vectors for improving siRNA delivery and gene silencing.

Degradation of mRNA by RNA interference is one of the most powerful and specific mechanisms for gene silencing. However, insufficient cellular uptake and poor stability have limited its usefulness. Here, we report efficient delivery of siRNA via the use of biodegradable nanoparticles (NPs) made from monomethoxypoly(ethylene glycol)-poly(lactic-co-glycolic acid)-poly-l-lysine (mPEG-PLGA-PLL) triblock copolymers. Various physicochemical properties of mPEG-PLGA-PLL NPs, including morphology, size, surface charge, siRNA encapsulation efficiency, and in vitro release profile of siRNA from NPs, were characterized by scanning electron microscope, particle size and zeta potential analyzer, and high performance liquid chromatography. The levels of siRNA uptake and targeted gene inhibition were detected in human lung cancer SPC-A1-GFP cells stably expressing green fluorescent protein. Examination of the cultured SPC-A1-GFP cells with fluorescent microscope and flow cytometry showed NPs loading Cy3-labeled siRNA had much higher intracellular siRNA delivery efficiencies than siRNA alone and Lipofectamine-siRNA complexes. The gene silencing efficiency of mPEG-PLGA-PLL NPs was higher than that of commercially available transfecting agent Lipofectamine while showing no cytotoxicity. Thus, the current study demonstrates that biodegradable NPs of mPEG-PLGA-PLL triblock copolymers can be potentially applied as novel non-viral vectors for improving siRNA delivery and gene silencing.

Profiling the Spatial Expression Pattern and ceRNA Network of lncRNA, miRNA, and mRNA Associated with the Development of Intermuscular Bones in Zebrafish.

Intermuscular bones (IBs) are small spicule-like bones in the muscular septum of fish, which affect their edible and economic value. The molecular mechanism of IB development is still uncertain. Numerous studies have shown that the ceRNA network, which is composed of mRNA, lncRNA, and miRNA, plays an important regulatory role in bone development. In this study, we compared the mRNA, lncRNA, and miRNA expression profiles in different IB development segments of zebrafish. The development of IBs includes two main processes, which are formation and growth. A series of genes implicated in the formation and growth of IBs were identified through gene differential expression analysis and expression pattern analysis. Functional enrichment analysis showed that the functions of genes implicated in the regulation of the formation and growth of IBs were quite different. Ribosome and oxidative phosphorylation signaling pathways were significantly enriched during the formation of IBs, suggesting that many proteins are required to form IBs. Several pathways known to be associated with bone development have been shown to play an important role in the growth of IBs, including calcium, ECM-receptor interaction, Wnt, TGF-ß, and hedgehog signaling pathways. According to the targeting relationship and expression correlation of mRNA, lncRNA, and miRNA, the ceRNA networks associated with the growth of IBs were constructed, which comprised 33 mRNAs, 9 lncRNAs, and 7 miRNAs. This study provides new insight into the molecular mechanism of the development of IBs.

Preparation of aripiprazole-poly(methyl vinyl ether-co-maleic anhydride) nanocomposites via supercritical antisolvent process for improved antidepression therapy.

Aripiprazole (ARI), a second-generation atypical antipsychotic drug approved for schizophrenia treatment, shows good efficacy against depression. However, the poorly aqueous solubility of ARI leads to low bioavailability and increased dose-related side effects, seriously limiting its application in pharmaceutics. Herein, we demonstrated the fabrication of ARI and poly (methyl vinyl ether-co-maleic anhydride) (PVMMA) composite nanoparticles (PA NPs) using the supercritical antisolvent (SAS) process for enhancing its water-solubility and curative anti-depressant effects. Initially, the optimal experimental conditions (ARI/PVMMA mass ratio of 1:6, pressure of 10 MPa, and solution flow rate of 0.75 ml min-1) were determined by a 23 factorial experimental design, resulting in the PA NPs with an excellent particle morphology. In vitro cell experiments showed that PA NPs significantly inhibited the inflammatory response caused by the microglia activation induced by lipopolysaccharide (LPS). Similarly, mice behavioral tests demonstrated that PA NPs significantly improved LPS-induced depression-like behavior. Importantly, compared with free ARI, the LPS-induced activation of microglia in the mouse brain and the expression of inflammatory factors in serum were significantly reduced after treatment with PA NPs. Together, the innovative PA NPs designed by SAS process might provide a candidate for developing new ARI-based nano-formulations.

Secreted in a Type III Secretion System-Dependent Manner, EsaH and EscE Are the Cochaperones of the T3SS Needle Protein EsaG of Edwardsiella piscicida.

The intracellular EscE protein tightly controls the secretion of the type III secretion system (T3SS) middle and late substrates in Edwardsiella piscicida. However, the regulation of secretion by EscE is incompletely understood. In this work, we reveal that EscE interacts with EsaH and EsaG. The crystal structures of the EscE-EsaH complex and EscE-EsaG-EsaH complex were resolved at resolutions of 1.4 Å and 1.8 Å, respectively. EscE and EsaH form a hydrophobic groove to engulf the C-terminal region of EsaG (56 to 73 amino acids [aa]), serving as the cochaperones of T3SS needle protein EsaG in E. piscicida. V61, K62, M64, and M65 of EsaG play a pivotal role in maintaining the conformation of the ternary complex of EscE-EsaG-EsaH, thereby maintaining the stability of EsaG. An in vivo experiment revealed that EscE and EsaH stabilize each other, and both of them stabilize EsaG. Meanwhile, either EscE or EsaH can be secreted through the T3SS. The secondary structure of EsaH lacks the fourth and fifth α helices presented in its homologs PscG, YscG, and AscG. Insertion of the α4 and α5 helices of PscG or swapping the N-terminal 25 aa of PscG with those of EsaH starkly decreases the protein level of the chimeric EsaH, resulting in instability of EsaG and deactivation of the T3SS. To the best of our knowledge, these data represent the first reported structure of the T3SS needle complex of pathogens from Enterobacteriaceae and the first evidence for the secretion of T3SS needle chaperones. IMPORTANCE Edwardsiella piscicida causes severe hemorrhagic septicemia in fish. Inactivation of the type III secretion system (T3SS) increases its 50% lethal dose (LD50) by ~10 times. The secretion of T3SS middle and late substrates in E. piscicida is tightly controlled by the intracellular steady-state protein level of EscE, but the mechanism is incompletely understood. In this study, EscE was found to interact with and stabilize EsaH in E. piscicida. The EscE-EsaH complex is structurally analogous to T3SS needle chaperones. Further study revealed that EscE and EsaH form a hydrophobic groove to engulf the C-terminal region of EsaG, serving as the cochaperones stabilizing the T3SS needle protein EsaG. Interestingly, both EscE and EsaH are secreted. Our study reveals that the EscE-EsaH complex controls T3SS protein secretion by stabilizing EsaG, whose secretion in turn leads to the secretion of the middle and late T3SS substrates.

Enhanced delivery of monomethoxypoly(ethylene glycol)-poly(lactic-co-glycolic acid)-poly l-lysine nanoparticles loading platelet-derived growth factor BB small interfering RNA by ultrasound and/or microbubbles to rat retinal pigment epithelium cells.

BACKGROUND: A novel small interfering RNA (siRNA) delivery method based on the combined use of nanoparticles (NPs) with ultrasound (US) and/or microbubbles (MBs) was introduced in the present study. We investigated the efficacy and safety of US and/or MBs-enhanced delivery of monomethoxypoly(ethylene glycol)-poly(lactic-co-glycolic acid)-poly l-lysine (mPEG-PLGA-PLL) NPs loading platelet-derived growth factor BB (PDGF-BB) siRNA to rat retinal pigment epithelium (RPE)-J cells. METHODS: The effect of US and/or MBs on the delivery of NPs containing Cy3-labeled siRNA was evaluated by fluorescence microscopy and flow cytometry. Potential toxicity of NPs and cell viability under different conditions of US and/or MBs were assessed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide method. RESULTS: The results obtained showed that low intensity US or 15-20% MBs could increase the delivery efficiency of a lower concentration of mPEG-PLGA-PLL NPs loading siRNA to RPE-J cells, whereas the combination of US with MBs under the optimal conditions for the enhancement of NPs delivery did not further increase the cellular uptake of NPs compared to either US or MBs alone (p = 0.072 and p = 0.488, respectively). Under the optimal condition for US-enhanced NPs delivery, the enhanced PDGF-BB gene silencing with a combination of US and NPs encapsulating siRNA resulted in a significant decrease of mRNA and protein expression levels compared to NPs alone. CONCLUSIONS: US and/or MBs could be used safely to enhance the delivery of NPs loading siRNA to rat RPE-J cells. A combination of the chemical (mPEG-PLGA-PLL NPs loading siRNA) and physical (US) approaches could more effectively downregulate the mRNA and protein expression of PDGF-BB.