PvGeneExpDB: An integrative gene expression database for in-depth understanding on the Pacific white shrimp (Litopenaeus vannamei).

The Pacific white shrimp (Litopenaeus vannamei) is a high-valued economic farming species. With the development of high-throughput sequencing technology, cumulative large-scale transcriptomic studies have been revealing molecular landscape of various biological conditions including genetic selection, breeding, evolution, disease landscape, etc. However, no single experiment or databases allow thorough investigations of transcriptomic dynamics for these progressions. Meanwhile, the available datasets are often scattered and lack management. Here, we have established PvGeneExpDB, the first gene expression database for L. vannamei (www.bio-marine-scau.com/pv_ex/), which encompasses gene expression profiles, differential expression, and co-expression analyses under various biological conditions. Based on the analyses of 7 datasets, which include 53 samples with accurate and detailed records, PvGeneExpDB identifies 20,599 novel transcripts, shows expression profiles of a total of 20,817 genes, and implements Gene Ontology (GO) reconstruction of 76.7 % of these genes. Besides, 26 co-expressed groups were first identified by large-scale, cross-sample Weighted Gene Co-expression Network Analysis (WGCNA). By integrating the gene expression data in the database, our goal is to deepen the biological understanding of L. vannamei.

Research on the construction of weaponry indicator system and intelligent evaluation methods.

To decrease subjective interference and improve the construction efficiency of the traditional weapon and equipment index system, an index system construction method based on target detection is proposed in combination with the equipment test video data. The three-level index system of combat effectiveness of a certain type of equipment is established, and various intelligent assessment methods are proposed. Firstly, an optimaized IPSO-BP network model is proposed, in which dynamic weights are set to improve the particle search network, and adaptive learning factors are introduced to optimize the update speed. Secondly, an improved DS evidence-parallel neural network assessment method is proposed, setting multiple parallel neural networks with different parameters, and improving the angle cosine to weaken the numerical nonlinear attributes in DS evidence fusion and increase the model's assessment operation stability. Thirdly, the three types of view features corresponding to the index item images are extracted to train the base classifiers. The integrated CNN network based multi-view feature integration assessment model is constructed and the improved residual network block is introduced to optimize the network gradient. Comparison with existing evaluation methods shows that the proposed methods achieve efficient and intelligent construction and evaluation of the indicator system and enrich the evaluation of indicator data.

Selective Antagonism of Lactiplantibacillus plantarum and Pediococcus acidilactici against Vibrio and Aeromonas in the Bacterial Community of Artemia nauplii.

Empiric probiotics are commonly consumed by healthy individuals as a means of disease prevention, pathogen control, etc. However, controversy has existed for a long time regarding the safety and benefits of probiotics. Here, two candidate probiotics, Lactiplantibacillus plantarum and Pediococcus acidilactici, which are antagonistic to Vibrio and Aeromonas species in vitro, were tested on Artemia under in vivo conditions. In the bacterial community of Artemia nauplii, L. plantarum reduced the abundance of the genera Vibrio and Aeromonas and P. acidilactici significantly increased the abundance of Vibrio species in a positive dosage-dependent manner, while higher and lower dosages of P. acidilactici increased and decreased the abundance of the genus Aeromonas, respectively. Based on the liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) analyses of the metabolite of L. plantarum and P. acidilactici, pyruvic acid was used in an in vitro test to explain such selective antagonism; the results showed that pyruvic acid was conducive or suppressive to V. parahaemolyticus and beneficial to A. hydrophila. Collectively, the results of this study demonstrate the selective antagonism of probiotics on the bacterial community composition of aquatic organisms and the associated pathogens. IMPORTANCE Over the last decade, the common preventive method for controlling potential pathogens in aquaculture has been the use of probiotics. However, the mechanisms of probiotics are complicated and mostly undefined. At present, less attention has been paid to the potential risks of probiotic use in aquaculture. Here, we investigated the effects of two candidate probiotics, L. plantarum and P. acidilactici, on the bacterial community of Artemia nauplii and the in vitro interactions between these two candidate probiotics and two pathogens, Vibrio and Aeromonas species. The results demonstrated the selective antagonism of probiotics on the bacterial community composition of an aquatic organism and its associated pathogens. This research contributes to providing a basis and reference for the long-term rational use of probiotics and to reducing the inappropriate use of probiotics in aquaculture.

Three-dimensional and single-cell sequencing of liver cancer reveals comprehensive host-virus interactions in HBV infection.

Backgrounds: Hepatitis B virus (HBV) infection is a major risk factor for chronic liver diseases and liver cancer (mainly hepatocellular carcinoma, HCC), while the underlying mechanisms and host-virus interactions are still largely elusive. Methods: We applied HiC sequencing to HepG2 (HBV-) and HepG2-2.2.15 (HBV+) cell lines and combined them with public HCC single-cell RNA-seq data, HCC bulk RNA-seq data, and both genomic and epigenomic ChIP-seq data to reveal potential disease mechanisms of HBV infection and host-virus interactions reflected by 3D genome organization. Results: We found that HBV enhanced overall proximal chromatin interactions (CIs) of liver cells and primarily affected regional CIs on chromosomes 13, 14, 17, and 22. Interestingly, HBV altered the boundaries of many topologically associating domains (TADs), and genes nearby these boundaries showed functional enrichment in cell adhesion which may promote cancer metastasis. Moreover, A/B compartment analysis revealed dramatic changes on chromosomes 9, 13 and 21, with more B compartments (inactive or closed) shifting to A compartments (active or open). The A-to-B regions (closing) harbored enhancers enriched in the regulation of inflammatory responses, whereas B-to-A regions (opening) were enriched for transposable elements (TE). Furthermore, we identified large HBV-induced structural variations (SVs) that disrupted tumor suppressors, NLGN4Y and PROS1. Finally, we examined differentially expressed genes and TEs in single hepatocytes with or without HBV infection, by using single-cell RNA-seq data. Consistent with our HiC sequencing findings, two upregulated genes that promote HBV replication, HNF4A and NR5A2, were located in regions with HBV-enhanced CIs, and five TEs were located in HBV-activated regions. Therefore, HBV may promote liver diseases by affecting the human 3D genome structure. Conclusion: Our work promotes mechanistic understanding of HBV infection and host-virus interactions related to liver diseases that affect billions of people worldwide. Our findings may also have implications for novel immunotherapeutic strategies targeting HBV infection.

Deciphering the virulent Vibrio harveyi causing spoilage in muscle of aquatic crustacean Litopenaeus vannamei.

The muscle of aquatic crustaceans is perishable and susceptible to environmental contamination. Vibrio harveyi is a widely occurring pathogen in aquatic animals. Here, bath treatment with a virulent V. harveyi strain (which was added directly in the rearing water to imitate environmental contamination) isolated from the muscle of the whiteleg shrimp, Litopenaeus vannamei, caused the muscle of Li. vannamei to display a whitish-opaque appearance due to microscopic changes including muscle lysis, muscle fiber damage and microbial colonization. When administered orally by incorporating this isolate in feed (which is an imitation of infection via natural route), rather than direct invasion followed by colonization in the muscle, this isolate indirectly stimulated severe muscle necrosis in Li. vannamei via steering the enrichment of two important (human) pathogens, V. cholerae and V. vulnificus, and one environmental bacterium Pseudomonas oleovorans, based on the meta-taxonomic analyses. In addition to the scientifically proven viral diseases, our research proved that bacterial agents are also capable of causing muscle spoilage in crustaceans via changing the microbial composition, and that the crustaceans might be exploited as the wide-spectrum sensitive bio-detector to indicate the extent of microbial contamination.

Role of myo-inositol supplementation against toxicity of excessive dietary copper in Pacific white shrimp Litopenaeus vannamei.

Raw materials for making dried shrimp (a type of foodstuff) are mostly from farmed shrimp and preliminary findings indicated that head copper (Cu) concentrations in some commercial dried shrimp products exceeded the safe limit specified in pollution-free aquatic products (50 mg/kg), which may influence food safety. Therefore, a 63-day feeding trial was conducted to explore effects of dietary Cu concentrations on accumulation of Cu in tissues, growth performance, immune response and antioxidant status of Pacific white shrimp (Litopenaeus vannamei). Moderating effect of myo-inositol (MI, adding 200 mg/kg diet) on the adverse impacts caused by excessive dietary Cu was also investigated. 600 shrimp (initial weight: 0.89 ± 0.00 g) were divided into five groups: 37.08 mg Cu/kg diet group (control group), 62.57 mg Cu/kg diet group, 125.99 mg Cu/kg diet group, 63.41 mg Cu/kg diet group (supplemented with MI) and 119.19 mg Cu/kg diet group (supplemented with MI). The results showed that dietary Cu concentrations increased from 37.08 to over 62.57 mg/kg, hepatopancreas Cu concentrations raised from 29.04 to 233.43-263.65 mg/kg, and muscle Cu concentrations only increased from 6.22 to 6.99-8.39 mg/kg. Report to control group, excessive Cu concentration (125.99 mg/kg) didn't significantly affect growth performance, but it notably reduced whole body lipid content and immune response, induced oxidative stress and damaged the hepatopancreas structure, which was ameliorated by MI supplementation. The results suggested that consuming shrimp head and its processed products weren't recommended. Cu concentrations of commercial feeds for Pacific white shrimp should be controlled below 62.57 mg/kg. Additionally, MI supplementation mitigated the negative impacts induced by excessive dietary Cu.

Probiotics: their action against pathogens can be turned around.

Probiotics when applied in complex evolving (micro-)ecosystems, might be selectively beneficial or detrimental to pathogens when their prophylactic efficacies are prone to ambient interactions. Here, we document a counter-intuitive phenomenon that probiotic-treated zebrafish (Danio rerio) were respectively healthy at higher but succumbed at lower level of challenge with a pathogenic Vibrio isolate. This was confirmed by prominent dissimilarities in fish survival and histology. Based upon the profiling of the zebrafish microbiome, and the probiotic and the pathogen shared gene orthogroups (genetic niche overlaps in genomes), this consequently might have modified the probiotic metabolome as well as the virulence of the pathogen. Although it did not reshuffle the architecture of the commensal microbiome of the vertebrate host, it might have altered the probiotic-pathogen inter-genus and intra-species communications. Such in-depth analyses are needed to avoid counteractive phenomena of probiotics and to optimise their efficacies to magnify human and animal well-being. Moreover, such studies will be valuable to improve the relevant guidelines published by organisations such as FAO, OIE and WHO.

A 4D flow cardiovascular magnetic resonance study of flow asymmetry and haemodynamic quantity correlations in the pulmonary artery.

OBJECTIVE: In this paper we elucidate the asymmetric flow pattern and the haemodynamic quantity distributions and correlations in the pulmonary artery (PA) vasculature in healthy adults having structurally normal hearts, to provide reference on the flow characteristics in the PA and the right ventricle. APPROACH: Velocity data are acquired non-invasively from 18 healthy volunteers by 4D flow magnetic resonance imaging, resolved to 20 phases with spatial resolution 3 × 3 × 3 mm3. Interpolation is applied to improve the accuracy in quantifying haemodynamic quantities including kinetic energy, rotational energy, helicity and energy dissipation rate. These quantities are volumetrically normalised to remove size dependency, representing densities or local intensity. MAIN RESULTS: Flow asymmetry in the PA is quantified in terms of all the flow dynamic quantities and their correlations. The right PA has larger diameter and higher peak stroke velocity than the left PA. It also has the highest rotational energy intensity. Counter-rotating helical streams in the main PA appear to be associated with the unidirectional helical flow noticed in the left and the right PA near the peak systole. SIGNIFICANCE: This study provides a fundamental basis of normal flow in the PA. It implies the validity to use these flow pattern-related quantitative measures to aid with the identification of abnormal PA flow non-invasively, specifically for detecting abnormalities in the pulmonary circulation and response to therapy, where haemodynamic flow is commonly characterised by increased vortical and helical formations.

Distribution of Geochemical Fractions of Phosphorus in Surface Sediment in Daya Bay, China.

Surface sediment samples were collected from 19 sites throughout Daya Bay, China, to study the concentrations, and spatial distributions of different fractions of phosphorus through sequential extraction methods. Like many coastal and marine areas, De-P was the dominant form of P, contributing 47.5% of TP, followed by O-P, contributing 25.5% of TP. Ex-P and Fe-P contribute the lowest to TP. The concentration of sedimentary TP ranged from 290.3~525.1 µg/g, with the average of 395.3 µg/g, which was a similar range to other estuaries and coastal areas. Based on the spatial distribution, Pearson correlation and Principal component analysis, different fractions of phosphorus showed different spatial distributions due to different sources. The molar ratio of organic carbon to phosphorus (TOC/O-P) ranged from 199 to 609, with the average of 413, which was much higher than the Redfield ratio, suggesting terrestrial sources of organic matter in Daya Bay surface sediment. The average bioavailable phosphorus was 149.6 µg/g and contributed 37.8% (24.6~56.0%) of TP, indicating that the surface sediments of Day Bay act as an important internal source of P.

Changes in growth performance, aflatoxin B1 residues, immune response and antioxidant status of Litopenaeus vannamei fed with AFB1-contaminated diets and the regulating effect of dietary myo-inositol supplementation.

This study aimed to investigate if myo-inositol (MI) supplementation could alleviate adverse effects caused by aflatoxin B1 (AFB1) with respect to growth performance, AFB1 residues, immune response and antioxidant status of Litopenaeus vannamei. 800 shrimp (initial weight: 1.1 g) were divided into five groups: MI0 (basal diet); MI0 + LA, MI0 + HA, MI200 + LA and MI200 + HA fed with AFB1-contaminated diets (LA, low concentration AFB1; HA, high concentration AFB1; MI200, adding 200 mg MI kg-1 diet). The results showed that HA significantly decreased growth performance, systemic inositol content and lipid content. AFB1 residues were detected in the hepatopancreas of shrimp, but not the muscle. Histological lesions were observed in MI0 + LA and MI0 + HA groups. HA supplementation raised malondialdehyde and protein carbonyl content and reduced some antioxidant enzyme activities and immune-related genes expression, which was slightly ameliorated by MI supplementation. Our results suggest that myo-inositol may slightly mitigate negative impacts caused by AFB1 in L. vannamei.

The role of flow rotation in the adult right atrium: a 4D flow cardiovascular magnetic resonance study.

OBJECTIVE: In healthy adults, the right atrium (RA) serves as a reservoir for the systemic flow return from the superior vena cava (SVC) and inferior vena cava (IVC), preparing the two flows to be transferred to the right ventricle (RV) and pulmonary circulation. This study aims to quantify the haemodynamics of the RA and the associated SVC and IVC inflows, which have not been fully understood to date. APPROACH: Eighteen adults with structurally normal hearts underwent 4D flow magnetic resonance imaging. The cardiac cycle was resolved to 20 temporal phases with a spatial resolution of 3 × 3 × 3 mm3. Analysis included objective visualisation of the flow structures in the RA identified by three different vortex identification criteria, kinetic energy (KE), enstrophy and dissipation. KE and helicity flux were also assessed in both caval veins. MAIN RESULTS: Vortex identification methods confirmed that in the majority of participants the blood flow from the caval veins filling the RA during ventricular systole is not chaotic, but rather forms an organised pattern of a single coherent forward turning vortex structure. Thirteen participants displayed a single vortex flow structure, four showed multiple vortices and one had a helical flow pattern without a clear vortex structure. A strong positive correlation exists between the flow KE and enstrophy density. SIGNIFICANCE: This suggests that flow energy in the RA is mainly rotational, part of which is convected by the highly helical SVC and IVC inflows. Multiple vortices tend to be associated with higher dissipation rates in the central RA region due to turbulence. The rotational nature of the flow in the RA maintains KE better than non-rotational flow. RA flow characteristics are highly related to the helicity content in the caval veins, as well as the KE flux intensity. Lower caval helicity or IVC KE flux dominance tends to favour single vortex formation while the opposite tends to lead to multiple vortices or the rare helical flow patterns. Atria lacking single vortex flow are inclined to have a larger energy input from atrial contraction.

Transcriptome analysis revealed changes of multiple genes involved in muscle hardness in grass carp (Ctenopharyngodon idellus) fed with faba bean meal.

An 8-week feeding trial and transcriptome analysis were conducted to investigate the potential mechanism of muscle-hardening caused by faba bean in grass carp (Ctenopharyngodon idellus). Ordinary grass carp (fed with practical diet) and crisp grass carp (fed with faba bean meal) groups were designed. Lower water holding capacity and higher some texture parameters were observed in the muscle of crisp grass carp compared with another group. 19.62 GB clean reads were generated, and total 1354 genes exhibiting differentially expression were identified (FDR < 0.05). Genes function enrichment revealed up-regulated genes in crisp grass carp mainly in response to myofibroblast proliferation, while down-regulated genes in response to immune regulation. Consistent with this, the tight junction pathway and the NF-κB signaling pathway were likewise significantly enriched. In summary, this study identified several candidate genes and putative signaling pathways deserving further investigation to the mechanism of muscle-hardening in fish fed with faba bean.

Intestinal Microbiota of Grass Carp Fed Faba Beans: A Comparative Study.

Many reports of the intestinal microbiota of grass carp have addressed the microbial response to diet or starvation or the effect of microbes on metabolism; however, the intestinal microbiota of crisp grass carp has yet to be elucidated. Moreover, the specific bacteria that play a role in the crispiness of grass carp fed faba beans have not been elucidated. In the present study, 16S sequencing was carried out to compare the intestinal microbiota in the fore-, mid- and hind-intestine segments of grass carp following feeding with either faba beans or formula feed. Our results showed that (1) the hind-intestine presented significant differences in diversity relative to the fore- or midintestine and (2) faba beans significantly increased the diversity of intestinal microbiota, changed the intestinal microbiota structure (Fusobacteria was reduced from 64.26% to 18.24%, while Proteobacteria was significantly increased from 17.75% to 51.99%), and decreased the metabolism of energy, cofactors and vitamins in grass carp. Furthermore, at the genus and species levels, Acinetobacter accounted for 15.09% of the microbiota, and Acinetobacter johnsonii and Acinetobacter radioresistens constituted 3.41% and 2.99%, respectively, which indicated that Acinetobacter of the family Moraxellaceae contributed to changes in the intestinal microbiota structure and could be used as a potential biomarker. These results may provide clues at the intestinal microbiota level to understanding the mechanism underlying the crispiness of grass carp fed faba beans.

Profiling kidney microRNAs from juvenile grass carp (Ctenopharyngodon idella) after 56days of oral exposure to decabromodiphenyl ethane.

Grass carp (Ctenopharyngodon idella) is one of the most important species in China. Decabromodiphenyl ethane (DBDPE) is a brominated flame retardant that has been used widely in industry, and has been observed to accumulate in the tissues of fish from South China. Evidence has shown that DBDPE is toxic to aquatic animals, but the molecular response has been unclear. MicroRNAs (miRNAs) are small noncoding and negative regulatory RNAs that are 20-24 nucleotides in length, which are involved in a wide range of biological processes. We took advantage of deep-sequencing techniques to accurately and comprehensively profile the kidney miRNA expression of grass carp after 8weeks of oral exposure to DBDPE. After mapping sequencing data to the genome and Expressed Sequence Tags (ESTs) of grass carp, we identified 493 miRNAs in the sequenced grass carp samples, which included 51 new miRNAs. The results indicated that 5 miRNAs were significantly down-regulated and 36 miRNAs were significantly up-regulated (FDR<0.001, 1.5-fold change) after DBDPE exposure. Real-time quantitative PCR (RT-qPCR) was performed on 4 miRNAs from the two samples, and the sequencing and RT-qPCR data were consistent. This study provides the first comprehensive identification of grass carp miRNAs, and the first expression analysis of grass carp miRNAs following DBDPE exposure. The results indicated that miRNAs have potential for use as biomarkers.

Role of P-glycoprotein and the intestine in the excretion of DPC 333 [(2R)-2-{(3R)-3-amino-3-[4-(2-methylquinolin-4-ylmethoxy)phenyl]-2-oxopyrrolidin-1-yl}-N-hydroxy-4-methylpentanamide] in rodents.

The role of the intestine in the elimination of (2R)-2-{(3R)-3-amino-3-[4-(2-methylquinolin-4-ylmethoxy)phenyl]-2-oxopyrrolidin-1-yl}-N-hydroxy-4-methylpentanamide (DPC 333), a potent inhibitor of tissue necrosis factor alpha-converting enzyme, was investigated in mice and rats in vivo and in vitro. In Madine-Darby canine kidney cells stably transfected with P-glycoprotein (P-gp) and DPC 333, the transport from B-->A reservoirs exceeded the transport from A-->B by approximately 7-fold. In Caco-2 monolayers and isolated rat ileal mucosa, DPC 333 was transported from basolateral to apical reservoirs in a concentration-dependent, saturable manner, and transport was blocked by N-(4-[2-(1,2,3,4-tetrahydro-6,7-dimethoxy-2-isoquinolinyl)ethyl]-phenyl)-9,10-dihydro-5-methoxy-9-oxo-4-acridine carboxamide (GF120918), confirming the contribution of P-gp/breast cancer resistance protein in B-->A efflux of DPC 333. In quantitative whole body autoradiography studies with [(14)C]DPC 333 in mice and rats, radioactivity was distributed throughout the small intestine in both species. In GF120918-pretreated bile duct-cannulated rats, radioactivity in feces was reduced 60%. Using the in situ perfused rat intestine model, approximately 20% of an i.v. dose of [(14)C]DPC 333 was measured in the intestinal lumen within 3 h postdose, 12% as parent. Kinetic analysis of data suggested that excreted DPC 333 may be further metabolized in the gut. Intestinal clearance was 0.2 to 0.35 l/h/kg. The above data suggest that in the rodent the intestine serves as an organ of DPC 333 excretion, mediated in part by the transporter P-gp.