Effects of dredging wastewater input history and aquaculture type on greenhouse gas fluxes from mangrove sediments along the shorelines of the Jiulong River Estuary, China.

Dredging wastewater (DW) from aquaculture ponds is a major disturbance factor in mangrove management, and its effects on the greenhouse gas (GHG) fluxes from mangrove sediment remain controversial. In this study, we investigated GHG (N2O, CH4, and CO2) fluxes from mangrove sediment at typical aquaculture pond-mangrove sites that were stimulated by DW discharged for different input histories and from different farm types. The GHG fluxes exhibited differing cumulative effects with increasing periods of DW input. The N2O and CH4 fluxes from mangrove sediment that received DW inputs for 17 y increased by ∼10 and ∼1.5 times, respectively, whereas the CO2 flux from mangrove sediment that received DW inputs for 11 y increased by ∼1 time. The effect of DW from shrimp ponds on the N2O flux was significantly larger than those of DW from fish/crab ponds and razor clam ponds. Moreover, the total global warming potentials (GWPs) at the field sites with DW inputs increased by 29-129% of which the CO2 flux was the main contributor to the GWP (85-96%). N2O as a proportion of CO2-equivalent flux increased from 2% to 12%, indicating that N2O was an important contributor to the increase in GWP. Overall, DW increased the GHG fluxes from mangrove sediments, indicating that the contribution of mangroves to climate warming was enhanced under DW input. It also implies that the carbon sequestration potential of mangrove sediments may be threatened to some extent. Therefore, future assessments of the carbon sequestration capacity of mangroves at regional or global scales should consider this phenomenon.

Y-mediated optimization of 3DG-PbO2 anode for electrochemical degradation of PFOS.

In our previous study, the three-dimensional graphene-modified PbO2 (3DG-PbO2) anode was prepared for the effective degradation of perfluorooctanesulfonat (PFOS) by the electrochemical oxidation process. However, the mineralization efficiency of PFOS at the 3DG-PbO2 anode still needs to be further improved due to the recalcitrance of PFOS. Thus, in this study, the yttrium (Y) was doped into the 3DG-PbO2 film to further improve the electrochemical activity of the PbO2 anode. To optimize the doping amount of Y, three Y and 3DG codoped PbO2 anodes were fabricated with different Y3+ concentrations of 5, 15, and 30 mM in the electroplating solution, which were named Y/3DG-PbO2-5, Y/3DG-PbO2-15 and Y/3DG-PbO2-30, respectively. The results of morphological, structural, and electrochemical characterization revealed that doping Y into the 3DG-PbO2 anode further refined the ß-PbO2 crystals, increased the oxygen evolution overpotential and active sites, and reduced the electron transfer resistance, resulting in a superior electrocatalytic activity. Among all the prepared anodes, the Y/3DG-PbO2-15 anode exhibited the best activity for electrochemical oxidation of PFOS. After 120 min of electrolysis, the TOC removal efficiency was 80.89% with Y/3DG-PbO2-15 anode, greatly higher than 69.13% with 3DG-PbO2 anode. In addition, the effect of operating parameters on PFOS removal was analyzed by response surface, and the obtained optimum values of current density, initial PFOS concentration, pH, and Na2SO4 concentration were 50 mA/cm2, 12.21 mg/L, 5.39, and 0.01 M, respectively. Under the optimal conditions, the PFOS removal efficiency reached up to 97.16% after 40 min of electrolysis. The results of the present study confirmed that the Y/3DG-PbO2 was a promising anode for electrocatalytic oxidation of persistent organic pollutants.

Loss of flrt2 gene leads to microphthalmia in zebrafish.

As a member of the fibronectin leucine-rich transmembrane (flrt) gene family, fibronectin leucine-rich transmembrane 2 (flrt2) is strongly expressed in a subset of sclerotome cells, and the resultant protein interacts with FGFR1 in the FGF signaling pathway during development. Studies on flrt2 have focused mainly on its roles in the brain, heart and chondrogenesis. However, reports on its expression and function in the zebrafish retina are lacking. Here, we detected the high expression of flrt2 in zebrafish retina using in situ hybridization technique and developed an flrt2-knockout (KO) zebrafish line using CRISPR/Cas9 genome editing. Quantitative real-time PCR was used to measure the expression levels of flrt2, which results in an approximately 60% mRNA reduction. The flrt2-KO zebrafish eyes' altered morphological, cellular, and molecular events were identified using BrdU labeling, TUNEL assay, immunofluorescent staining, fluorescent dye injection and RNA sequencing. Abnormal eye development, known as microphthalmia, was found in flrt2-KO larvae, and the retinal progenitor cells exhibited increased apoptosis, perhaps owing to the combined effects of crx, neurod4, atoh7, and pcdh8 downregulation and Casp3a and Caspbl upregulation. In contrast, the retinal neural development, as well as retinal progenitor cell differentiation and proliferation, were not affected by the flrt2 deletion. Thus, flrt2 appears to play important roles in retinal development and function, which may provide the basis for further investigations into the molecular mechanisms of retinal development and evolution.

An improved graph Laplacian regularization method for identifying biomarkers of Alzheimer's disease.

Alzheimer's disease (AD) is one of the most common dementia, and its pathogenesis has not been clarified. The failure of amyloid targeted therapy has led us to rethink the pathogenesis of AD. There is growing evidence that complex diseases usually involve the impairment of multiple biological functions, rather than focus on several single genes. Protein-protein interaction network (PPIN) has been recognized as an important tool for identifying and predicting disease biomarkers. It is a great challenge to design network-based classification method for identifying effective, stable and interpretable biomarkers to distinguish the disease phenotype based on gene expression profile data. In this study, we used graph Laplacian regularization method to introduce topology information of PPIN, which can reveal the damaged networks involved in disease from heterogeneous gene expression profile data and identify disease-related biomarkers. The results in three AD datasets showed that the biomarkers identified by our method can not only distinguish the sample categories more accurately, but also help researchers understand the biological meaning behind complex diseases.

Molecular characterization and functional analysis of peroxiredoxin 4 in grass carp (Ctenopharyngodon idella).

Peroxiredoxins (Prxs) are a group of evolutionarily conserved selenium-independent thiol-specific antioxidant proteins. In this study, the peroxiredoxin-4 (CiPrx4) gene from grass carp was identified and characterized. The full-length of CiPrx4 is 1339 bp, encoding 260 amino acids that contain two peroxiredoxin signature motifs and two GVL motifs. CiPrx4 belongs to the typical 2-Cys subfamily and shows the highest homology with Prx4 from Cyprinus carpio (95.4%). CiPrx4 mRNA was constitutively expressed in all tested tissues and was upregulated by grass carp reovirus and pathogen-associated molecular pattern (PAMP) stimulation. CiPrx4 was localized in the cytoplasm and co-localized with the endoplasmic reticulum. The purified CiPrx4 protein protected DNA from degradation in a dose-dependent manner. Moreover, the overexpression of CiPrx4 in Escherichia coli and fish cells showed apparent antioxidant and antiviral activities. Collectively, the results of the present study provide new insights for further understanding the functions of Prx4 in teleost fish.

A Correlation Analysis between SNPs and ROIs of Alzheimer's Disease Based on Deep Learning.

Motivation. At present, the research methods for image genetics of Alzheimer's disease based on machine learning are mainly divided into three steps: the first step is to preprocess the original image and gene information into digital signals that are easy to calculate; the second step is feature selection aiming at eliminating redundant signals and obtain representative features; and the third step is to build a learning model and predict the unknown data with regression or bivariate correlation analysis. This type of method requires manual extraction of feature single-nucleotide polymorphisms (SNPs), and the extraction process relies on empirical knowledge to a certain extent, such as linkage imbalance and gene function information in a group sparse model, which puts forward certain requirements for applicable scenarios and application personnel. To solve the problems of insufficient biological significance and large errors in the previous methods of association analysis and disease diagnosis, this paper presents a method of correlation analysis and disease diagnosis between SNP and region of interest (ROI) based on a deep learning model. It is a data-driven method, which has no obvious feature selection process. Results. The deep learning method adopted in this paper has no obvious feature extraction process relying on prior knowledge and model assumptions. From the results of correlation analysis between SNP and ROI, this method is complementary to other regression model methods in application scenarios. In order to improve the disease diagnosis performance of deep learning, we use the deep learning model to integrate SNP characteristics and ROI characteristics. The SNP feature, ROI feature, and SNP-ROI joint feature were input into the deep learning model and trained by cross-validation technique. The experimental results show that the SNP-ROI joint feature describes the information of the samples from different angles, which makes the diagnosis accuracy higher.

A Novel Three-Stage Framework for Association Analysis Between SNPs and Brain Regions.

Motivation: At present, a number of correlation analysis methods between SNPs and ROIs have been devised to explore the pathogenic mechanism of Alzheimer's disease. However, some of the deficiencies inherent in these methods, including lack of statistical efficacy and biological meaning. This study aims at addressing issues: insufficient correlation by previous methods (relative high regression error) and the lack of biological meaning in association analysis. Results: In this paper, a novel three-stage SNPs and ROIs correlation analysis framework is proposed. Firstly, clustering algorithm is applied to remove the potential linkage unbalanced structure of two SNPs. Then, the group sparse model is used to introduce prior information such as gene structure and linkage unbalanced structure to select feature SNPs. After the above steps, each SNP has a weight vector corresponding to each ROI, and the importance of SNPs can be judged according to the weights in the feature vector, and then the feature SNPs can be selected. Finally, for the selected feature SNPS, a support vector machine regression model is used to implement the prediction of the ROIs phenotype values. The experimental results under multiple performance measures show that the proposed method has better accuracy than other methods.

Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain.

Common carp is one of the oldest and most popular cultured freshwater fish species both globally and in China. In a previous study, we used a carp strain with a long breeding tradition in China, named Huanghe, to create a new fast-growing strain by selection for fast growth for 6 years. The growth performance at 8 months of age has been improved by 20.84%. To achieve this, we combined the best linear unbiased prediction with marker-assisted selection techniques. Recent progress in genome-wide association studies and genomic selection in livestock breeding inspired common carp breeders to consider genome-based breeding approaches. In this study, we developed a 2b-RAD sequence assay as a means of investigating the quantitative trait loci in common carp. A total of 4,953,017,786 clean reads were generated for 250 specimens (average reads/specimen = 19,812,071) with BsaXI Restriction Enzyme. From these, 56,663 SNPs were identified, covering 50 chromosomes and 3,377 scaffolds. Principal component analysis indicated that selection and control groups are relatively clearly distinct. Top 1% of Fst values was selected as the threshold signature of artificial selection. Among the 244 identified loci, genes associated with sex-related factors and nutritional metabolism (especially fat metabolism) were annotated. Eighteen QTL were associated with growth parameters. Body length at 3 months of age and body weight (both at 3 and 8 months) were controlled by polygenic effects, but body size (length, depth, width) at 8 months of age was controlled mainly by several loci with major effects. Importantly, a single shared QTL (IGF2 gene) partially controlled the body length, depth, and width. By merging the above results, we concluded that mainly the genes related to neural pathways, sex and fatty acid metabolism contributed to the improved growth performance of the new Huanghe carp strain. These findings are one of the first investigations into the potential use of genomic selection in the breeding of common carp. Moreover, our results show that combining the Fst, QTL mapping and CRISPR-Cas9 methods can be an effective way to identify important novel candidate molecular markers in economic breeding programs.

Responses of Different Cancer Cells to White Tea Aqueous Extract.

White tea from the eastern Chinese province of Fujian is a unique tea variety. Although the health effects of various teas have been investigated in recent years, most studies focused exclusively on green tea varieties. In order to study effects exerted by white tea from eastern Fujian on the viability of cancer cells, we analyzed its main bioactive ingredients. We also evaluated the antioxidant activity of white tea aqueous extract (WTAE) and employed MTT assay to evaluate effects of WTAE on viabilities of Hela and BEL-7402 cancer cell lines. Apoptosis rate detection was also applied to estimate efficacy of cellular apoptotic induction by WTAE in these two cells types. Results revealed that WTAE exhibited high antioxidant activity and inhibited effectively the proliferation of Hela and BEL-7402 cells. The half maximal inhibitory concentration (IC50) of WTAE for Hela cells (0.05 mg/mL) was lower than that for BEL-7402 cells (0.1 mg/mL). Although WTAE induced apoptosis in both cell lines, pro-apoptotic effects were markedly more apparent in Hela cells. Our study demonstrated that WTAE inhibited proliferation of cancer cells via induction of apoptosis and that Hela cells were more sensitive to WTAE than BEL-7402 cells. PRACTICAL APPLICATION: The aim of this study is to provide a new approach toward cancer prevention by consuming white tea, the properties of which may also be helpful in formulating novel anticancer therapeutics.

Heterogeneity Analysis and Diagnosis of Complex Diseases Based on Deep Learning Method.

Understanding genetic mechanism of complex diseases is a serious challenge. Existing methods often neglect the heterogeneity phenomenon of complex diseases, resulting in lack of power or low reproducibility. Addressing heterogeneity when detecting epistatic single nucleotide polymorphisms (SNPs) can enhance the power of association studies and improve prediction performance of complex diseases diagnosis. In this study, we propose a three-stage framework including epistasis detection, clustering and prediction to address both epistasis and heterogeneity of complex diseases based on deep learning method. The epistasis detection stage applies a multi-objective optimization method to find several candidate sets of epistatic SNPs which contribute to different subtypes of complex diseases. Then, a K-means clustering algorithm is used to define subtypes of the case group. Finally, a deep learning model has been trained for disease prediction based on graphics processing unit (GPU). Experimental results on pure and heterogeneous datasets show that our method has potential practicality and can serve as a possible alternative to other methods. Therefore, when epistasis and heterogeneity exist at the same time, our method is especially suitable for diagnosis of complex diseases.

Comparative transcriptome analysis of zebrafish (Danio rerio) brain and spleen infected with spring viremia of carp virus (SVCV).

Spring viremia of carp virus (SVCV) is the pathogen of spring viremia of carp (SVC) and often causes acute hemorrhagic symptoms in various kinds of cyprinids and induces serious environmental and economic losses. However, the molecular mechanisms of infection remain poorly understood, especially at the individual level. In this study, zebrafish was employed as the infection model to explore the pathogenesis of SVCV. 4 groups of zebrafish tissues were set and RNA sequencing (RNA-Seq) technology was employed to analyze the differentially expressed genes (DEGs) after SVCV-infection. A total of 360,971,498 clean reads were obtained from 12 samples, 382 DEGs in the brain and 926 DEGs in the spleen were identified. These DEGs were annotated into three ontologies after gene ontology (GO) enrichment analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these DEGs were primarily related to Influenza A pathway and Herpes simplex infection pathway in brain and Tuberculosis and Toxoplasmosis pathways in spleen, and all of these pathways may be involved in response to pathogen invasion. At the same time, 3' and 5' alternative splicing (AS) events were significantly up-regulated in the spleen. The transcriptome analysis results demonstrated changes and tissue-specific influences caused by SVCV in vivo, which provided us with more information to understand the complex relationships between SVCV and its host.

Zebrafish Health Conditions in the China Zebrafish Resource Center and 20 Major Chinese Zebrafish Laboratories.

In China, the use of zebrafish as an experimental animal in the past 15 years has widely expanded. The China Zebrafish Resource Center (CZRC), which was established in 2012, is becoming one of the major resource centers in the global zebrafish community. Large-scale use and regular exchange of zebrafish resources have put forward higher requirements on zebrafish health issues in China. This article reports the current aquatic infrastructure design, animal husbandry, and health-monitoring programs in the CZRC. Meanwhile, through a survey of 20 Chinese zebrafish laboratories, we also describe the current health status of major zebrafish facilities in China. We conclude that it is of great importance to establish a widely accepted health standard and health-monitoring strategy in the Chinese zebrafish research community.

MicroRNA profile analysis of Epithelioma papulosum cyprini cell line before and after SVCV infection.

MicroRNAs (miRNAs) play significant roles in regulating almost all of the biological processes in eukaryotes. An accumulating body of evidence shows that miRNAs are associated with cellular changes following viral infection. Spring viremia of carp virus (SVCV) is the pathogen of Spring viremia of carp (SVC), which results in heavy losses in the cultured common carp (Cyprinus carpio) industry in many countries. To study the involvement of miRNAs during SVCV infection, we adopted the Solexa sequencing technology to sequence small RNA libraries from the Epithelioma papulosum cyprini (EPC) cell line before and after infection with SVCV. In this study, a total of 161 conserved and 26 novel miRNAs were identified. Subsequently, the expression patterns of these miRNAs were compared between the uninfected (control library, M) and SVCV-infected (infection library, E) libraries. In addition, to verify the Solexa sequencing results, the expression patterns of 14 randomly selected miRNAs were validated by qRT-PCR. The targets of the significantly differentially expressed miRNAs were then predicted, and the miRNAs that could directly target the SVCV genome were also predicted. No miRNA encoded by SVCV itself was detected. To the best of our knowledge, this study presents the first miRNA profiling assessment in association with fish rhabdovirus infection, and the data presented lay a foundation for further investigations to determine the roles of miRNAs in regulating the molecular mechanism during SVCV infection.

Spring viraemia of carp virus induces autophagy for necessary viral replication.

Outbreaks of spring viraemia of carp virus (SVCV) in several carp species and other cultivated fish can cause significant mortality and jeopardize the billion-dollar worldwide fish industry. Spring viraemia of carp virus, also known as Rhabdovirus carpio, is a bullet-shaped RNA virus that enters and amplifies in gill epithelium and later spreads to internal organs. Young fish under stressed conditions (spring cold water, etc.) are more vulnerable to SVCV-induced lethality because of their lack of a mature immune system. Currently, the host response of SVCV remains largely unknown. Here, we observed that autophagy is activated in SVCV-infected epithelioma papulosum cyprini (EPC) cells. We demonstrated that the SVCV glycoprotein, rather than viral replication, activates the autophagy pathway. In addition, SVCV utilized the autophagy pathway to facilitate its own genomic RNA replication and to enhance its titres in the supernatants. Autophagy promoted the survival of SVCV-infected cells by eliminating damaged mitochondrial DNA generated during viral infection. We further showed that SVCV induces autophagy in EPC cells through the ERK/mTOR signalling pathway. Our results reveal a connection between autophagy and SVCV replication and propose autophagy suppression as a novel means to restrict SVCV viral replication.

The interaction between ß1 integrins and ERK1/2 in osteogenic differentiation of human mesenchymal stem cells under fluid shear stress modelled by a perfusion system.

Fluid shear stress (FSS) is an important biomechanical factor regulating the osteogenic differentiation of human mesenchymal stem cells (hMSCs) and is therefore widely used in bone tissue engineering. However, the mechanotransduction of FSS in hMSCs remains largely unknown. As ß1 integrins are considered to be important mechanoreceptors in other cells, we suspect that ß1 integrins should also be important for hMSCs to sense the stimulation of FSS. We used a perfusion culture system to produce FSS loading on hMSCs seeded in PLGA three-dimensional (3D) scaffolds and investigated the roles of ß1 integrins, FAK and ERK1/2 in FSS-induced osteogenic differentiation of hMSCs. Our results showed that FSS not only markedly increased ALP activity and the expression of ALP, OCN, Runx2 and COLIα genes but also significantly enhanced the phosphorylation of ERK1/2, Runx2 and FAK. FSS-induced activation of ERK1/2 and FAK was inhibited by blockade of the connection between ß1 integrins and ECM with RGDS peptide and integrins ß1 monoclonal antibody. Our study also found that FSS could upregulate the expression level of ß1 integrins and that this upregulation could be abolished by PD98059. Further investigation indicated that FSS-activated ERK1/2 led to the phosphorylation of IκBα and NFκB p65. The activation of NFκB p65 resulted in the upregulation of ß1 integrin expression. Therefore, it could be inferred that ß1 integrins should sense the stimulation of FSS and thus activate ERK1/2 through activating of FAK, and FSS-activated ERK1/2 feedback to upregulate the expression of ß1 integrins through activating NFκB.

Proteomic analysis of epithelioma papulosum cyprini cells infected with spring viremia of carp virus.

Spring viremia of carp (SVC), caused by spring viremia of carp virus (SVCV) is an important disease due to its drastic effects on carp fisheries in many countries. To better understand molecular responses to SVCV infection, two dimensional electrophoresis (2-DE) and MALDI-TOF/TOF were performed to investigate altered proteins in epithelioma papulosum cyprini cells (EPCs). Differentially expressed proteins in mock-infected EPCs and SVCV-infected EPCs were compared. A total of 54 differentially expressed spots were successfully identified (33 up-regulated spots and 21 down-regulated spots) which include cytoskeleton proteins, macromolecular biosynthesis-associated proteins, stress response proteins, signal transduction proteins, energy metabolism, and ubiquitin proteasome pathway-associated proteins. Moreover, 7 corresponding genes of the differentially expressed proteins were quantified using real time RT-PCR to examine their transcriptional profiles. The presence of four selected cellular proteins (beta-actin, gamma1-actin, heat shock cognate 71 kDa protein and annexin A2) associated with the spring viremia of carp virus (SVCV) particles was validated by Western blot assay. This study provides dynamic and useful protein-related information to further understand the underlying pathogenesis of SVCV infection.

Biological, immunological and regenerative characteristics of placenta-derived mesenchymal stem cell isolated using a time-gradient attachment method.

It has been verified that placenta contains multi-lineage mesenchymal stem cells (MSCs). We have used a time-gradient attachment method to isolate placenta-derived MSCs (PMSCs). The morphology, differentiation potential, immunogenicity and xenogenic reconstruction potential of these PMSCs were examined. The results showed that PMSCs isolated using the time-gradient attachment method showed higher potential of in vitro proliferation and multi-lineage differentiation. PMSCs isolated using the time-gradient attachment method showed a low immunogenicity. HLA-A gene fragment and no HLA-DR gene fragment were detected in PMSCs isolated using the time-gradient attachment method, and the mixed lymphocyte reaction (MLR) assay identified that these cells inhibited the proliferation of the allogeneic T-lymphocytes induced by PHA. The transplantation in calvaria of rats showed that PMSCs had the higher xenogenic reconstruction potential. Finally, the significance of PMSCs isolated using the time-gradient attachment method in experimental and clinical applications is discussed.

Functionalized self-assembled monolayers on mesoporous silica nanoparticles with high surface coverage.

Mesoporous silica nanoparticles (MSNs) containing vinyl-, propyl-, isobutyl- and phenyl functionalized monolayers were reported. These functionalized MSNs were prepared via molecular self-assembly of organosilanes on the mesoporous supports. The relative surface coverage of the organic monolayers can reach up to 100% (about 5.06 silanes/nm.

Hepatogenic engineering from human bone marrow mesenchymal stem cells in porous polylactic glycolic acid scaffolds under perfusion culture.

Bone marrow mesenchymal stem cells (MSCs) are promising candidates for cell therapy and tissue engineering. We used mesenchymal stem cells from human bone marrow (hMSCs) as the seeding cells to investigate the potential of hepatocytic differentiation of hMSCs in porous polylactic glycolic acid (PLGA) scaffolds under perfusion induction. hMSCs were seeded and proliferated in PLGA scaffolds, and then induced into hepatocyte-like cells with hepatogenic medium in perfusion and static cultures. The results showed that hMSCs could be induced into hepatocyte-like cells in PLGA scaffolds with hepatogenic medium in both static and perfusion induction systems. However, perfusion induction was more effective for cellularity in PLGA scaffolds than in static induction. Cells in the scaffold induced by the hepatogenic medium expressed hepatocyte-specific genes cytokeratin 19 (CK19), α-fetoprotein (αFP), cytokeratin 18 (CK18), albumin and cytochrome P4503A4 (CYP3A4) in a time-dependent manner. Induced cells stained positive for αFP and albumin. Induced cells also acquired the functional characteristics of hepatocytes, i.e. secretion of urea and albumin. In a comparison of survival and hepatogenic differentiation of hMSCs between perfusion and static induction, perfusion induction increased the survival and the uniform distribution of induced cells in scaffolds, which resulted in a higher efficiency of hepatogenesis in the PLGA construct with hMSCs. The oscillatory perfusion induction system combined with the hepatogenic medium should be a valuable and convenient tool for in vitro hepatic tissue engineering using hMSCs.