Fusarium graminearum rapid alkalinization factor peptide negatively regulates plant immunity and cell growth via the FERONIA receptor kinase.

The plant rapid alkalinization factor (RALF) peptides function as key regulators in cell growth and immune responses through the receptor kinase FERONIA (FER). In this study, we report that the transcription factor FgPacC binds directly to the promoter of FgRALF gene, which encodes a functional homologue of the plant RALF peptides from the wheat head blight fungus Fusarium graminearum (FgRALF). More importantly, FgPacC promotes fungal infection via host immune suppression by activating the expression of FgRALF. The FgRALF peptide also exhibited typical activities of plant RALF functions, such as inducing plant alkalinization and inhibiting cell growth, including wheat (Triticum aestivum), tomato (Solanum lycopersicum) and Arabidopsis thaliana. We further identified the wheat receptor kinase FERONIA (TaFER), which is capable of restoring the defects of the A. thaliana FER mutant. In addition, we found that FgRALF peptide binds to the extracellular malectin-like domain (ECD) of TaFER (TaFERECD) to suppress the PAMP-triggered immunity (PTI) and cell growth. Overexpression of TaFERECD in A. thaliana confers plant resistance to F. graminearum and protects from FgRALF-induced cell growth inhibition. Collectively, our results demonstrate that the fungal pathogen-secreted RALF mimic suppresses host immunity and inhibits cell growth via plant FER receptor. This establishes a novel pathway for the development of disease-resistant crops in the future without compromising their yield potential.

Identification of sex chromosome and sex-determining gene of southern catfish (Silurus meridionalis) based on XX, XY and YY genome sequencing.

Teleosts are important models to study sex chromosomes and sex-determining (SD) genes because they present a variety of sex determination systems. Here, we used Nanopore and Hi-C technologies to generate a high-contiguity chromosome-level genome assembly of a YY southern catfish (Silurus meridionalis). The assembly is 750.0 Mb long, with contig N50 of 15.96 Mb and scaffold N50 of 27.22 Mb. We also sequenced and assembled an XY male genome with a size of 727.2 Mb and contig N50 of 13.69 Mb. We identified a candidate SD gene through comparisons to our previous assembly of an XX individual. By resequencing male and female pools, we characterized a 2.38 Mb sex-determining region (SDR) on Chr24. Analysis of read coverage and comparison of the X and Y chromosome sequences showed a Y specific insertion (approx. 500 kb) in the SDR which contained a male-specific duplicate of amhr2 (named amhr2y). amhr2y and amhr2 shared high-nucleotide identity (81.0%) in the coding region but extremely low identity in the promotor and intron regions. The exclusive expression in the male gonadal primordium and loss-of-function inducing male to female sex reversal confirmed the role of amhr2y in male sex determination. Our study provides a new example of amhr2 as the SD gene in fish and sheds light on the convergent evolution of the duplication of AMH/AMHR2 pathway members underlying the evolution of sex determination in different fish lineages.

Antimicrobial behavior and mechanism of clove oil nanoemulsion.

Clove oil has many functions such as antibacterial, anti-inflammatory, anti-oxidation. In this experiment, a self-emulsification method was used to prepare clove oil nanoemulsion. And then filter paper diffusion method, minimum inhibitory concentration, and minimum bactericidal concentration were used to study the inhibitory behavior of clove oil nanoemulsion on Escherichia coli and Staphylococcus aureus. And explore the antibacterial mechanism by dynamically testing the content of nucleic acid and protein in the culture solution during the antibacterial process. The results show that when the surfactant content is 10 wt%, the hydrophile-lipophile balance (HLB) is 13.93, and the oil phase content is 2 wt%, a clove oil nanoemulsion with better dispersion and smaller average particle size can be prepared. The minimum inhibitory concentration (MIC) of clove oil nanoemulsion against Escherichia coli and Staphylococcus aureus is 0.5, 0.25 mg/mL, and the minimum bactericidal concentration (MBC) is 1, 2 mg/mL. The increase in protein content and the exponential growth of nucleic acid release also indicated that the clove oil nanoemulsion destroys the integrity of the cell membrane. The experimental results can provide a reference for the application of clove oil nanoemulsion in food, medicine and other fields.

Structural characterization and antibacterial properties of konjac glucomannan/soluble green tea powder blend films for food packaging.

Antimicrobial activity is a promising property for food packaging which could prolong the shelf life of food products. In this paper, the physicochemical and antimicrobial properties of konjac glucomannan (KGM)/soluble green tea powder (SGTP) edible films were firstly prepared and analyzed through light barrier properties, Fourier transform infrared spectroscopy (FT-IR), tensile strength (TS), X-ray diffraction (XRD), thermogravimetric analysis and scanning electron microscope (SEM). The results showed that appropriate addition of SGTP could improve the TS of composite films. With the increase of SGTP content, the transmittance of the films in the ultraviolet region decreased obviously, and the thermal stability was improved in a SGTP dependent manner. KGM/SGTP films present a fairly smooth and flat surface without any fracture when 0.5% SGTP was provided. The bacteriostatic test showed that the bacteriostatic performance of the composite films against Staphylococcus aureus and Escherichia coli was also significantly enhanced. When 1% SGTP was provided, the zones of inhibition for Escherichia coli and Staphyloccocus aureus reached to 13.45 ± 0.94 mm and 13.76 ± 0.92 mm, respectively. Overall, the KGM/SGTP films showed great potential as bioactive packaging materials to extend food shelf life.

Identification, Expression and Evolution of Short-Chain Dehydrogenases/Reductases in Nile Tilapia (Oreochromis niloticus).

The short-chain dehydrogenases/reductases (SDR) superfamily is involved in multiple physiological processes. In this study, genome-wide identification and comprehensive analysis of SDR superfamily were carried out in 29 animal species based on the latest genome databases. Overall, the number of SDR genes in animals increased with whole genome duplication (WGD), suggesting the expansion of SDRs during evolution, especially in 3R-WGD and polyploidization of teleosts. Phylogenetic analysis indicated that vertebrates SDRs were clustered into five categories: classical, extended, undefined, atypical, and complex. Moreover, tandem duplication of hpgd-a, rdh8b and dhrs13 was observed in teleosts analyzed. Additionally, tandem duplications of dhrs11-a, dhrs7a, hsd11b1b, and cbr1-a were observed in all cichlids analyzed, and tandem duplication of rdh10-b was observed in tilapiines. Transcriptome analysis of adult fish revealed that 93 SDRs were expressed in more than one tissue and 5 in one tissue only. Transcriptome analysis of gonads from different developmental stages showed that expression of 17 SDRs were sexually dimorphic with 11 higher in ovary and 6 higher in testis. The sexually dimorphic expressions of these SDRs were confirmed by in situ hybridization (ISH) and qPCR, indicating their possible roles in steroidogenesis and gonadal differentiation. Taken together, the identification and the expression data obtained in this study contribute to a better understanding of SDR superfamily evolution and functions in teleosts.

Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia.

Ribosomal proteins (RPs) are indispensable in ribosome biogenesis and protein synthesis, and play a crucial role in diverse developmental processes. In the present study, we carried out a comprehensive analysis of RPs in chordates and examined the expression profiles of the complete set of 92 cytoplasmic RP genes in Nile tilapia. The RP genes were randomly distributed throughout the tilapia genome. Phylogenetic and syntenic analyses revealed the existence of duplicated RP genes from 2R (RPL3, RPL7, RPL22 and RPS27) and 3R (RPL5, RPL19, RPL22, RPL41, RPLP2, RPS17, RPS19 and RPS27) in tilapia and even more from 4R in common carp and Atlantic salmon. The RP genes were found to be expressed in all tissues examined, but their expression levels differed among different tissues. Gonadal transcriptome analysis revealed that almost all RP genes were highly expressed, and their expression levels were highly variable between ovaries and testes at different developmental stages in tilapia. No sex- and stage-specific RP genes were found. Eleven RP genes displayed sexually dimorphic expression with nine higher in XY gonad and two higher in XX gonad at all stages examined, which were proved to be phenotypic sex dependent. Quantitative real-time PCR and immunohistochemistry ofRPL5b and RPL24 were performed to validate the transcriptome data. The genomic resources and expression data obtained in this study will contribute to a better understanding of RPs evolution and functions in chordates.

Identification and Evolution of TGF-ß Signaling Pathway Members in Twenty-Four Animal Species and Expression in Tilapia.

Transforming growth factor ß (TGF-ß) signaling controls diverse cellular processes during embryogenesis as well as in mature tissues of multicellular animals. Here we carried out a comprehensive analysis of TGF-ß pathway members in 24 representative animal species. The appearance of the TGF-ß pathway was intrinsically linked to the emergence of metazoan. The total number of TGF-ß ligands, receptors, and smads changed slightly in all invertebrates and jawless vertebrates analyzed. In contrast, expansion of the pathway members, especially ligands, was observed in jawed vertebrates most likely due to the second round of whole genome duplication (2R) and additional rounds in teleosts. Duplications of TGFB2, TGFBR2, ACVR1, SMAD4 and SMAD6, which were resulted from 2R, were first isolated. Type II receptors may be originated from the ACVR2-like ancestor. Interestingly, AMHR2 was not identified in Chimaeriformes and Cypriniformes even though they had the ligand AMH. Based on transcriptome data, TGF-ß ligands exhibited a tissue-specific expression especially in the heart and gonads. However, most receptors and smads were expressed in multiple tissues indicating they were shared by different ligands. Spatial and temporal expression profiles of 8 genes in gonads of different developmental stages provided a fundamental clue for understanding their important roles in sex determination and reproduction. Taken together, our findings provided a global insight into the phylogeny and expression patterns of the TGF-ß pathway genes, and hence contribute to the greater understanding of their biological roles in the organism especially in teleosts.

Bioinformatic analyses of zona pellucida genes in vertebrates and their expression in Nile tilapia.

Zona pellucida (ZP) genes encode ZP glycoproteins which constitute the coat surrounding oocytes and early embryos. Genome-wide identification of ZP genes is still lacking in vertebrates, especially in fish species. Herein, we conducted bioinformatic analyses of the ZP genes of the Nile tilapia and other vertebrates. Totally 16, 9, 17, 27, 21, 20, 26, 19, 14,11, 24, 17, 9, 18, 8, 11, 9, 8, 5, and 4 ZP genes belonging to 5 subfamilies (ZPA, ZPB, ZPC, ZPD, and ZPAX) were found in the sea lamprey, elephant shark, coelacanth, spotted gar, zebrafish, medaka, stickleback, Nile tilapia, Amazon molly, platyfish, seahorse, Northern snakehead, cavefish, tetraodon, clawed frog, turtle, chicken, platypus, kangaroo rat, and human genomes, respectively. The expansion of ZP genes in basal vertebrates was mainly achieved by gene duplication of ZPB, ZPC, and ZPAX subfamilies, while the shrink of ZP gene number in viviparous mammals was achieved by keeping only one copy of the ZP genes in each subfamily or even secondary loss of some subfamilies. The number of ZP gene is related to the environment where the eggs are fertilized and the embryos develop in vertebrates. Transcriptomic analysis showed that 14 ZP genes were expressed in the ovary of Nile tilapia, while two (ZPB2b and ZPC2) were highly expressed in the liver. On the other hand, ZPB1a and ZPB2c were not found to be expressed in any tissue or at any developmental stage of the gonads examined. In the ovary, the expression of ZP genes started from 30 dah (days after hatching), significantly upregulated at 90 dah and maintained this level at 180 dah. The expression of ZPC2 in the liver and ZPC5-2 and ZPAX1 in the ovary was confirmed by in situ hybridization. The ovary- and liver-expressed ZP genes are expressed coordinately with oocyte growth in tilapia.

Characterization of the male-specific region containing the candidate sex-determining gene in Amur catfish (Silurus asotus) using third-generation- and pool-sequencing data.

Amur catfish (Silurus asotus) is an ecologically and economically important fish species in Asia. Here, we assembled the female and male Amur catfish genomes, with genome sizes of 757.15 and 755.44 Mb, respectively, at the chromosome level using nanopore and Hi-C technologies. Consistent with the known diploid chromosome count, both genomes contained 29 chromosome-size scaffolds covering 98.80 and 98.73 % of the complete haplotypic assembly with scaffold N50 of 28.87 and 27.29 Mb, respectively. The female (n = 40) and male (n = 40) pools were re-sequenced. Comparative analysis of sequencing and re-sequencing data from both sexes confirmed the presence of an XX/XY sex determination system in Amur catfish and revealed Chr5 as the sex chromosome containing an approximately 400 kb Y-specific region (MSY). Gene annotation revealed a male-specific duplicate of amhr2, namely amhr2y, in MSY, which is male-specific in different wild populations and expressed only in the testes. Amur catfish shared partially syntenic MSY and amhr2y genes with the southern catfish (S. meridionalis, Chr24), which were located on different chromosomes. High sequence divergence between amhr2y and amhr2 and high sequence similarity with amhr2y were observed in both species. These results indicate the common origin of the sex-determining (SD) gene and transition of amhr2y in the two Silurus species. Accumulation of repetitive elements in the MSY of both species may be the main driver of the transition of amhr2y. Overall, our study provides valuable catfish genomic resources. Moreover, determination of amhr2y as the candidate SD gene in Amur catfish provides another example of amhr2 as the SD gene in fish.

Influence of Anhydrite on the Properties and Microstructure of Aluminophosphate Cement.

Aluminophosphate cement (APC) is a new type of hydraulic cementitious material with many potential functions. Microscopic analysis techniques were used to study the effect of anhydrite on the performance and hydration process of APC under standard curing conditions. The results show that adding an appropriate amount of anhydrite promotes the hydration of APC. The highest compressive strength is reached at an anhydrite content of 15 wt.%. As the anhydrite content increases, the APC's compressive strength decreases. The microscopic analysis of the hydration product morphology shows that the incorporation of anhydrite produces ettringite and other hydration products, improving the microstructure of the cement paste. The mercury intrusion porosimetry results show that the total porosity of the hardened APC paste decreases, and the microstructure becomes denser with an increase in the curing age, resulting in an increase in the compressive strength over time.

Response of the chemical structure of soil organic carbon to modes of maize straw return.

Elucidating the chemical structure of soil organic matter (SOM) is important for accurately evaluating the stability and function of SOM. Aboveground vegetation directly affects the quantity and quality of exogenous organic matter input into the soil through plant residues and root exudates, which in turn affects soil microbial species, community structure, and activity, and ultimately impacts the chemical structure of SOM. In this study, a 13C nuclear magnetic resonance technique was used to analyze the chemical structure characteristics of soil organic carbon (SOC) under various rates of straw returning combined with rotary tillage and under full straw mulching. The results showed that full straw returning with rotary tillage and full straw mulching more effectively increased the SOC content than reduced rate of straw returning (1/2 and 1/3 of full straw) with rotary tillage. The contents of alkyl C and alkoxy C in the functional groups of SOC under various straw returning treatments were increased compared with those under the treatment of maize stubble remaining in soil (CK). Furthermore, the contents of aromatic C and carboxyl C were decreased, which were consistent with the chemical shift changes of SOC. Compared with CK treatment, straw returning decreased the content of aromatic C in the functional groups of SOC, but increased the content of alkoxy C, which could be associated with the change in integral areas of absorption peaks of alkyl C and alkoxy C moving toward left and right, respectively. The content of total SOC was significantly positively (P < 0.05) correlated with that of alkoxy C and significantly negatively (P < 0.01) correlated with that of aromatic C. The molecular structure of SOC tends to be simplified due to the decreasing in refractory C and the increasing in easily decomposed C after straw returning to the field.

High Internal-Phase Pickering Emulsions Stabilized by Xanthan Gum/Lysozyme Nanoparticles: Rheological and Microstructural Perspective.

Food-grade high internal-phase Pickering emulsions (HIPPEs) stabilized by solid or colloidal particles with different advantages have attracted extensive attention nowadays. However, looking for new appropriate particle stabilizers is the common practice for HIPPEs preparation. It is crucial to find a new strategy for the development of functional HIPPEs with controllable properties. In this study, a high concentration of xanthan gum/lysozyme nanoparticles (XG/Ly NPs) was used for the preparation of HIPPEs for the first time. Visual observations, creaming index (CI), microstructure, and rheology tests were carried out to investigate the potential of XG/Ly NPs as HIPPEs stabilizers. Results indicated that XG/Ly NPs could stabilize oil droplets in the concentration range of 0.5-4% (w/v). The HIPPEs with a minimal particle concentration of 1% exhibited remarkable physical stability. Rheological measurements showed that a high stability of solid-like HIPPEs was successfully obtained with a higher concentration of XG/Ly NPs. Overall, the HIPPEs stabilized by different concentrations of XG/Ly NPs exhibited excellent rheological and structural properties, which might provide a feasible strategy for the development of functional emulsion systems with controllable structures.

Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles.

The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.

Stability, microstructural and rheological properties of Pickering emulsion stabilized by xanthan gum/lysozyme nanoparticles coupled with xanthan gum.

Effects of xanthan gum (XG) addition and oil contents on the structural and rheological properties of Pickering emulsion stabilized by xanthan gum/Lysozyme nanoparticles (XG/Ly NPs) were analyzed by microstructure, creaming index, and rheological analysis. The results showed that XG addition reduced the droplet size of the emulsion, and a denser three-dimensional network structure was formed between droplets in the continuous phase. Thus, the migration of droplets slowed down, and the stability of Pickering emulsion increased. Rheological studies indicated that the network structure of Pickering emulsion depends on XG addition and oil content. The critical strain (γco) displayed three regimes. For low oil content (20%), γco decreased with the increase of XG concentration. For Pickering emulsion with medium oil content (40%, v/v), γco increased with increasing addition of XG. When high oil content (60-80%) was provided, γco was almost independent of XG addition. The results showed that the microstructure, stability and rheological properties of Pickering emulsion stabilized by XG/Ly NPs could be regulated by XG addition and oil content. This attempt provided theoretical support for regulating Pickering emulsion properties by polysaccharides addition, and established Pickering emulsions with various demands.

Genome-wide identification, evolution of ATF/CREB family and their expression in Nile tilapia.

The ATF/CREB family of transcription factors represents a large group of basic region-leucine zipper (bZip) proteins that regulate diverse cellular responses. Here we carried out a comprehensive analysis of ATF/CREB family members in 22 representative animal species. The family probably originated from the early diverging metazoan and significantly expanded in vertebrates due to multiple whole genome duplication. Duplicates of atf6 were derived from 2R, and duplicates of creb1, crem, jdp2, creb5, atf4, atf5 and atf7 were products of 3R. We also isolated 21 ATF/CREBs, belonging to 6 subfamilies from Nile tilapia. Based on transcriptome data, most members were found to be dominantly expressed in the head kidney, heart, brain and testis. Some ATF/CREBs displayed sexual dimorphic expression in gonad at 5, 90 and 180 dah (days after hatching), but not at 30 dah. creb1a and atf4a were found to be expressed mainly in phase I and II oocytes of the ovary; while creb1b and atf4b mainly in spermatogenic cells of the testis, indicating divergence of duplicated genes from 3R which suggested neofunctionalization or subfunctionalization in gonad. This is the first genome-wide screening and evolutionary analysis of ATF/CREB family in different animals, particularly in teleosts. The expression analysis of this family in tilapia gonad provided a fundamental clue for understanding their important roles in sex differentiation and gonadal development in teleosts.

The cross correlation properties of composite systems.

A new method is presented for characterizing cross correlations in composite systems described by a couple of time-dependent random variables. This method is based on (i) rescaling the time derivatives of the variables to make their variances unity and then (ii) recombining these rescaled variables into their sum and difference. This manipulation enables one to express the joint probability distribution function in a peculiar way. It is also found that the entropy of composite systems is not equal to the sum of entropy of each subsystem because of the cross correlations.

Genome-wide identification, evolution of chromobox family genes and their expression in Nile tilapia.

Chromobox (Cbx) family proteins are transcriptional repressors that involved in epigenetic and developmental processes. In this study, comprehensive analyses of Cbxs were performed using available genome databases from representative animal species. The Cbx family were originated from one Polycomb (Pc) gene like the yeast Pc, which duplicated into two and gave rise to the Pc and the Heterochromatin protein 1 (Hp1) identified in invertebrates from protozoon to lancelet. Rapid expansion of Cbx family members was observed in vertebrates as ~8 (5 Pc and 3 Hp1) were identified in spotted gar, coelacanth and tetrapods. Further expansion of the members to ~14 (9 Pc and 5 Hp1) was observed in teleosts due to the third round genome duplication (3R). Based on transcriptome data from eight adult tilapia tissues, most of the Cbxs were found to be dominantly expressed in the brain, testis, ovary and heart. Analyses of the gonadal transcriptome data from four developmental stages revealed that all Cbxs were expressed in both ovary and testis except Cbx7b, with significant increase of the total and average RPKM from 5 to 90dah (days after hatching). By in situ hybridization, the three most highly and sexual dimorphically expressed Cbx genes in gonads, Cbx1b, Cbx3a and Cbx5, were found to be expressed in phase I and II oocytes of the ovary, and in secondary spermatocytes (Cbx1b and Cbx3a) and spermatids (Cbx5) of the testis. Our results revealed the evolution of Cbx genes and indicated a potential role of Cbxs in epigenetic regulation of gametogenesis.