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• A new method developed for ancestral expression inference which can deal with various transcriptome data. • R package, AnceTran , which can perform transcriptome evolution analysis. • A case study for RNA-seq and ChIP-seq data analysis in mice species. With the help of high-throughput NGS (next-generation sequencing) technologies, ancestral transcriptome reconstruction is helpful to understand the complexity of transcriptional regulatory systems that underlies the evolution of multiple cellular metazoans with sophisticated functions and distinctive morphologies. To this end, we report a new method of ancestral state inference. The new method used Ornstein-Uhlenbeck (OU) model, which is more biologically realistic, to replace the Brownian motion (BM) model and is suitable for multi-transcriptome data. Implemented in the free R package, AnceTran is specially designed for RNA-seq and ChIP-seq data, which is feasible. It should be noticed that our work will be integrated to a unified, statistically-sound phylogenetic framework to study the evolution of many other molecular phenomes such as proteomics, chromatin accessibility, methylation status, and metabolomics. We exemplify our method by a case study, using the ChIP-seq binding data of three liver-specific transcription factors and the RNA-seq liver expression data in four closely related mice species, and some technical issues are discussed. [ABSTRACT FROM AUTHOR]

Abstract MicroRNAs (miRNAs) are emerging as important regulators of neurodegenerative diseases. However, research into ocular intracellular miRNAs, though possessing great potential to uncover novel and valuable therapeutic targets for glaucoma, is only at an early stage. Here we show that expression levels of miR-211 were significantly induced in aqueous humor (AH) samples from patients with glaucoma when compared to normal AH samples. Notably, oxidative stress-elicited miR-211 potentiated high pressure-induced retinal ganglion cells (RGCs) death by impairing ERK activation but enhancing P38 activation, an effect mediated by direct downregulation of fibroblast growth factor receptor substrate 2 (Frs2) signaling pathway in a sequence complementarity-dependent fashion. In support of the concept of a fundamental connection between miR-211 upregulation and augmented pressure-induced cell death in RGCs, we showed that ectopic expression of the exogenous FRS2 was sufficient to neutralize the miR-211-induced decrease in the cell viability and significantly improved miR-211-inhibited cell survival, in high pressure-challenged RGC-5 cells. Together, our findings show that miR-211 negatively modulates cell survival programs upon high pressure challenge by regulating Frs2 signaling, and they define roles for miR-211/Frs2 cascade in a regulatory feedback loop that mediates the pathogenesis of glaucoma. Highlights • miR-211 expression is upregulated in aqueous humor samples from glaucoma patients. • Oxidative stress induces miR-211 expression in retinal ganglion cells (RGCs). • miR-211 potentiates high pressure-induced RGCs death via distinct MAPK pathways. • miR-211 directly targets Frs2 3′UTR in RGCs. [ABSTRACT FROM AUTHOR]

• Facial emotion recognition (FER) is associated with multiple speech communication disorders (SCD). • Based on language evaluation and eye-tacking experiment, strong and detailed correlations were found between different dimensions of speech communication ability and various eye-movement patterns. • A machine-learning-based SCD prediction model was designed to screen SCD (accuracy as high as 88.9%). • A group of FER gazing patterns was found to be highly sensitive to the possibility of children's SCD. The ability of efficient facial emotion recognition (FER) plays a significant role in successful human communication and is closely associated with multiple speech communication disorders (SCD) in children. Despite the relevance, little is known about how speech communication abilities (SCA) and FER are correlated or of their underlying mechanism. To address this, we monitored eye movements of 115 children while watching human faces with different emotions and designed a machine-learning based SCD prediction model to explore the underlying pattern of eye movements during the FER task as well as their correlation with SCA. Strong and detailed correlations were found between different dimensions of SCA and various eye-movement features. A group of FER gazing patterns was found to be highly sensitive to the possibility of children's SCD. The SCD prediction model reached an accuracy as high as 88.9%, which offers a possible technique to fast screen SCD for children. [ABSTRACT FROM AUTHOR]

Cathepsin L, a lysosomal endopeptidase, has been noted for its involvement in the innate immune response in invertebrates. Here, the cathepsin L cDNA of the sea cucumber Apostichopus japonicus ( Aj CatL) is identified from an EST library and then cloned by the rapid amplification of the cDNA ends (RACE) PCR. The full-length cDNA is 1678 bp long containing an open reading frame (ORF) of 1002 bp, an 80 bp 5′ UTR and a 599 bp 3′ UTR. The cDNA encodes 333 amino acid residues with a predicted molecular mass of 37.07 kDa and a theoretical isoelectric point (pI) of 5.01. The full-length Aj CatL contains three active sites of eukaryotic thiol (cysteine) protease at positions 133–144, 278–288 and 295–314. Analysis of the predicted tertiary structure of prepro-CatL (17–333 aa) and mature-CatL (116–333 aa) reveals that the propeptide region (17–115 aa) blocks access to the substrate-binding cleft. Phylogenetic analysis shows that the Aj CatL is clustered together with two other CatLs from Strongylocentrotus purpuratus . The enzymatic activity of Aj CatL was verified using a substrate hydrolyzing assay with recombinant m Aj CatL. Further analysis of real time-PCR demonstrates that the expression of Aj CatL mRNA is significantly up-regulated in the coelomocytes in cases of infection with the common bacterial pathogen, Vibrio splendidus . This suggests that the Aj CatL is likely to be involved in the immune response. [ABSTRACT FROM AUTHOR]

Hydrological management of the Three Gorges Dam has resulted in the interception of heavy metals in the Three Gorges Reservoir (TGR). However, the exposure to heavy metals and health risks among local residents remained poorly understood. Here we collected 208 biomarker samples (hair) and 20 food species from typical regions in the TGR to assess the exposure levels of three toxic metals (Cr, Pb and As) in residents of the TGR, and subsequently investigated their health risk via dietary intake. Results indicated that hair Cr and As levels were below the reference value for normal people and threshold of skin lesions, respectively, whereas about 22% hair Pb exceeded the reference for clinical medicine, indicating a potential Pb exposure of local residents. Smoking habit and fish consumption were found to be predictors for hair Pb. In addition, the concentrations of heavy metals in all investigated food samples were below the limits of contaminants in food in China, except for Pb in the sweet potato and fish. The estimated daily intake of metals (DIMs) revealed that the intakes of Cr and As from studied food were under the recommended thresholds of Cr and As. However, the intake of Pb via diet exceeded the limit of the prevalence of chronic kidney disease and closed to the threshold for cardiovascular, which was probably associated with the high Pb concentrations of fish and sweet potato. Overall, residents around the TGR were at low exposure to Cr and As, but Pb exposure may need more attention. [Display omitted] • Residents in the TGR area were at low Cr and As exposures. • Residents in the TGR area might be at a potential Pb exposure. • The daily intakes of Cr and As were low, while Pb needed more attention. [ABSTRACT FROM AUTHOR]

Hypothesis Anionic surfactants can form stable monolayers around oil droplets via interactions with macromolecules thereby physically stabilizing high fish oil enriched emulsions (50–70% fish oil) while phenolic acids have antioxidant properties to prevent lipid oxidation. COSMO-RS ( Co nductor-like S creening M odel for R eal S olvents) is a powerful tool for the rational design of molecules with multi-functionalities. Therefore, it should be possible to assemble segments of natural molecules into a single multifunctional molecule using COSMO-RS to confer both physical and oxidative stability to fish oil enriched systems. Experiments COSMO-RS was used to predict the thermodynamic properties of series phenoleoyl malic acid esters of monoglycerides in comparison with commercial emulsifiers. A novel series of amphiphilic lipids, equipped with multi-functional groups from natural building blocks (fatty-acyl, glycerol, malic & phenolic acids), were then synthesized in a facile approach and characterized by various spectroscopy techniques. Oil-in-water emulsions stabilized by the amphiphilic lipids were formulated and characterized by dynamic light scattering measurements and fluorescence imaging. Findings An elaborate integration of multi-functions into a single molecule was achieved, displaying superior or comparable emulsion stability and antioxidant property, compared to a commercial emulsifier, phenolic acids and their combinations. This is the first report to holistically integrate the rational design, synthesis and functional characterization of natural-based multifunctional molecules for high capacity fish oil delivery systems. [ABSTRACT FROM AUTHOR]

Scavenger receptors (SRs) are crucial pattern recognition receptors (PRRs) to defense pathogen infection in fish innate immunity. In this paper, some members in SRs family of Larimichthys crocea were identified, including eight genes in the class A, B, D and F families. (G + C) % of all SRs members held 51% ∼ 59%, and these genes were no obvious codon bias by analyzing the distribution of A-, T-, G- and C-ended codons. The order of Enc for all SRs members by sequencing was LycCD68 > LycSCARA5 > LycSCARB1 > LycCD163 > LycMARCO > LycSREC1 > LycSCARA3 > LycSREC2 . Moreover, different lengths and numbers of exons and introns led to the diverse mRNAs and respective functional domains or motifs, for example, an optional cysteine-rich (SRCR) domain in LycMARCO and LycSCARA5 , an epidermal growth factor (EGF) and EGF-like domain in LycSREC1 and LycSREC2 . The sub-cellular localization demonstrated SRs members mainly located in plasma membrane or extracellular matrix. Further, all of the SRs members in L. crocea were almost low expressed in heart, gill and intestine, whereas high in spleen and liver. After stimulation by Vibrio alginolyticus , the class A and F families were induced significantly, but the class B and D families expressed less even none after pathogenic infection. All the findings would pave the way to understand not only the evolution of the SR-mediated immune response, but also the complexity of fish immunity. [ABSTRACT FROM AUTHOR]

[Display omitted] • In vitro self-assembly of leucine zipper fusion enzymes. • d -Phg is completely converted to l -Phg, with the ee% of 99%. • Bioinformatics analysis and changes in activation and bond energies. Amino acid transferase is a family of enzymes used to catalyze and separate chiral amino acids. However, due to the low efficiency, by-products and reverse reactions occur in cascade reactions. Therefore, in the research, phenylglycine aminotransferase and aspartate aminotransferase were self-assembled in vitro by leucine zipper. The self-assembled enzyme system with d -phenylglycine and α-ketoglutarate as substrates were used for the chiral transformation reaction. By studying the enzyme combination, kinetic reaction stability and catalytic efficiency, it was found that the self-assembled enzyme showed improved stability and better affinity to the substrate than the control and achieved only ee value of 17.86% for the control at the substrate ratio was 1:2. In contrast, the self-assembled enzyme basically catalyzed the complete conversion of d -Phg to l -Phg, with the ee value as 99%. These results demonstrated the feasibility of the leucine zipper and the conversion of d -phenylglycine to the l -type by fusion enzyme. [ABSTRACT FROM AUTHOR]

Chiral amino acids and their deamination products, α-keto acids, have important applications in food, medicine, and fine chemicals. In this study, two l -amino acid deaminase genes from Proteus mirabilis , PM473 of type Ⅰ and PM471 of type Ⅱ were cloned and expressed in Escherichia coli respectively, expected to achieve the chiral separation of amino acids. Extensive substrate preference testing showed that both deaminases had catalytic effects on the d -amino acid component of the D, l -amino acids, and PM473 has a wider catalytic range for amino acids. When D, L-Cys was used as the substrate, all L-Cys components and 75.1 % of D-Cys were converted to mercapto pyruvate, and the remaining D-Cys was a single chiral enantiomer. Molecular docking analysis showed that the interaction between the substrate and the key residues affected the stereoselectivity of enzymes. The compatibility of hydrophobicity between the binding pocket and substrate may be the basic factor that affects the substrate selectivity. This work provides an alternative method for the production of α-keto acids and the resolution of chiral amino acids. • L-AADs might work better on D-amino acids when catalyzing D, L-amino acids simultaneously. • PM471 was sensitive to the reaction conditions and the ee s could reach 100% when it catalyzed mixed cysteine. • The compatibility of hydrophobicity and stability of structure between the binding pocket and substrate may affect the enzyme selectivity. [ABSTRACT FROM AUTHOR]

• Perceiving natural poetic sentences with strong prosodic regularities requires lower brain workload but wider functional networks with long-range connections comparing to non-poetic speech. • Long-reaching hubs are elicited by integrated sentence-level speech perception in the right hemisphere. • Poetic speeches promote the auditory perception-to-production circuit in children, which decreases with ages. • The positive correlation between neural sensitivity of poetic speeches and behavioral speech ability indicates its role on facilitating early speech development. Natural poetic speeches (i.e., proverbs, nursery rhymes, and commercial ads) with strong prosodic regularities are easily memorized by children and the harmonious acoustic patterns are suggested to facilitate their integrated sentence processing. Do children have specific neural pathways for perceiving such poetic utterances, and does their speech development benefit from it? We recorded the task-induced hemodynamic changes of 94 children aged 2 to 12 years using functional near-infrared spectroscopy (fNIRS) while they listened to poetic and non-poetic natural sentences. Seventy-three adult as controls were recruited to investigate the developmental specificity of children group. The results indicated that poetic sentences perceiving is a highly integrated process featured by a lower brain workload in both groups. However, an early activated large-scale network was induced only in the child group, coordinated by hubs for connectivity diversity. Additionally, poetic speeches evoked activation in the phonological encoding regions in the children's group rather than adult controls which decreases with children's ages. The neural responses to poetic speeches were positively linked to children's speech communication performance, especially the fluency and semantic aspects. These results reveal children's neural sensitivity to integrated speech perception which facilitate early speech development by strengthening more sophisticated language networks and the perception-production circuit. [ABSTRACT FROM AUTHOR]

The sea cucumber Apostichopus japonicus is dioecious, with seasonal reproduction. G protein-coupled receptor (GPCR)-mediated signaling systems might play critical roles in the reproductive control of A. japonicus. Here, we classified GPCR from the genome in silico and used transcriptomic analyses to further mine those that function in gonadal-development control. Totally, 487 GPCRs were predicted from A. japonicus , and 183 of these were further annotated to molecular pathways. Transcriptome analysis revealed 327 GPCRs expressed in gonads, and these were classified into four families and 19 subfamilies. Three pathways were apparently associated with reproduction, including neuroactive ligand-receptor interaction, the mTOR and Wnt signaling pathways. Seven and eight ovary- and testis-specific GPCRs were filtered, and the gene expression profiles were determined in multiple tissues and gonads at different developmental stages by qPCR. These results provide new insights into the discovery of GPCR-mediated signaling control in sea cucumber reproduction, especially in gonadal development control. • 487 G protein-coupled receptors are predicted and classified from Apostichopus japonicus. • A variety of G protein-coupled receptors are detected to be expressed in the gonads of Apostichopus japonicus. • Gonad-specific G protein-coupled receptors have been screened out. [ABSTRACT FROM AUTHOR]

Abstract Interleukin-8 (IL-8 or chemokine (C-X-C motif) ligand 8, CXCL8) is a chemokine produced by multiple cell types. It promotes chemotaxis and phagocytosis via interaction with chemokine receptors CXCR1 and CXCR2. Using published data, IL-8 gene (LcIL-8) of the large yellow croaker (Larimichthys crocea) was cloned into the pcDNA3.1 plasmid, and an interleukin-8 receptor (LcCXCR2) was cloned into the pEGFP-N1 plasmid. Secratory expression of Lc IL-8 in HEK293T cells was carried out, and product in culture medium was collected for Lc CXCR2 stimulation in HEK293 cells. Following receptor internalization observation and intracellular signaling detection, the functional interaction of Lc IL-8 and Lc CXCR2 was further determined and the ERK phosphorylation signal activation mediated by Lc CXCR2 was demonstrated. Quantitative real-time PCR analysis was used to analyze transcription level regulation of Lc IL-8 and Lc CXCR2 in various tissues of large yellow croaker. Expression of LcIL-8 and LcCXCR2 was elevated in the spleen, head kidney, and liver after Vibrio parahemolyticus challenge. Results illustrated the functional interaction between Lc IL-8 and Lc CXCR2 in mediating intracellular ERK1/2 phosphorylation signaling and suggested that the Lc IL-8 and Lc CXCR2 system is part of the immune response induced by V. Parahemolyticus in L. crocea. Highlights • The full length CDS of Lc CXCR2 from spleen of large yellow croaker was cloned. • The cell surface localization of Lc CXCR2 was determinated. • Fusion expression of Lc IL-8 and Lc CXCR2 was conducted in HEK293T and HEK293 cells. • The functional inteaction between Lc IL-8 and Lc CXCR2 was demonstrated and their immunoregulatory function has been revealed. [ABSTRACT FROM AUTHOR]

Polylactide (PLA)/layered double hydroxide (LDH) films with good flame retardant property and transparency were synthesized by solution exfoliation and film casting method. The organic–inorganic interfacial interaction between PLA and NiAl-LDH was carefully modified by 2-carboxylethyl-phenyl-phosphinic acid (CEPPA) to well solve the dispersion problem of NiAl-LDH nanolayers and get enhanced flame retardancy of PLA composites. The results showed the NiAl-LDH/CEPPA (LC) nanolayers had exfoliated structures and were homogenously dispersed in PLA matrixes. All the PLA/LDH films had good transparency even LC content was up to 10 wt%. The PLA/LDH films absorbed the ultraviolet light, which alleviates the embrittlement of PLA films in the using procedure. The flame retardant effect characterized by microscale combustion calorimeter was observed when LC contents increased. The total heat release value of the sample with 10 wt% LC decreased to 9.7 kJ/g from 12.0 kJ/g of virgin PLA. [ABSTRACT FROM AUTHOR]