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Cirriformia species usually inhabit intertidal zones and deep-sea sediments. Their accurate identification has proven to be challenging. Here, we present the complete mitochondrial genome of one Cirriformia tentaculata_Montagu 1808 specimen collected from China. The total length of the complete mitochondrial sequence of C. tentaculata is 15,516 bp and consists of 13 protein-coding genes (PCGs), 23 tRNA genes, two rRNA genes, and an A + T rich region (64.20%). All PCGs begin with the typical ATN start codon, except for cox1, which uses TTG. TAA or TAG serve as termination codons for twelve PCGs, while nad5 terminates with an incomplete codon, T. The phylogenetic tree revealed a close relationship between C. tentaculata in this study, and Cirriformia cf. tentaculata and Timarete posteria from Korea. The information will assist in the future identification and understanding of this species and offers a novel point of reference for identifying Cirriformia species, and phylogenetic studies. [ABSTRACT FROM AUTHOR]

The application of waste rubber powder (WRP) for asphalt pavement could achieve the harmless and resourceful utilization of solid waste, but the storage stability of waste rubber powder modified asphalt (RA) is one of the main problems restricting its application. Existing studies have demonstrated that graphene could enhance the storage stability of RA, but graphene's size effect on the modifying effect and its corresponding mechanism are still uncertain. In this research, the effects of graphene microstructural properties (i.e., molecular size and layer number) on the storage stability of RA were investigated by storage stability testing, dynamic shear rheometry (DSR) testing and fluorescence microscopy (FM) testing, in combination with molecular dynamics simulation (MD). The experimental results indicated that graphene improved the storage stability of RA significantly, with few-layer graphene being more effective in enhancing it. MD was used to investigate the graphene size effect on RA in compatibility, intermolecular binding energy and structural stability of the system. The simulation results revealed that small-sized graphene molecules were more compatible with RA. Meanwhile, few-layer, small-sized graphene can provide higher binding energy and better enhancement of storage stability of RA. The number of graphene layers mainly influences the binding energy rather than solubility parameters. The relative concentration distribution results demonstrated that graphene facilitated the spatial distribution of asphaltenes, rubber components and light components. This research provides theoretical support for the rational selection of microstructural properties of graphene to improve the modified asphalt storage stability performance. [ABSTRACT FROM AUTHOR]

Bacillus spp. could be one of the most suitable substitutes for the control and prevention of aquatic diseases. The occurrence of species population, antimicrobial character, and virulence diversity in Bacillus spp. recovered from the mariculture system in China between 2009 and 2021 were investigated, screening for probiotic Bacillus strains with good biological safety that can inhibit Vibrio parahaemolyticus, V. alginolyticus, V. harveyi, V. owensii, V. campbellii. The results showed that 116 Bacillus isolates were divided into 24 species, and the top three species were B. subtilis (37/116), B. velezensis (28/116), and B. amyloliquefaciens (10/116). Among the 116 Bacillus isolates, 32.8% were effective against V. parahaemolyticus, 30.1% for V. alginolyticus, 60.3% for V. harveyi, 69.8% for V. owensii and 74.1% for V. campbellii. More than 62% of Bacillus isolates were susceptible to florfenicol, doxycycline and tetracycline, etc., and 26/116 Bacillus isolates were found to be multiple-antibiotic-resistant (MAR), with MARI values ranging from 0 to 0.06. Eighteen kinds of antibiotic resistance genes were tested; only tetB, blaTEM, and blaZ were detected. And 9 isolates in 2 Bacillus species were excluded by 6/10 kinds of Bacillus-related toxin gene (hblA, hblC, nheB, nheC, entFM, cykK). Bio-safety testing indicated that three kinds of probiotics were good probiotic candidates to prevent Vibriosis. These results provide comprehensive genetic diversity, potential risks, and probiotic characteristics of Bacillus in the mariculture system in China, and provide basic support for green and healthy development of aquatic industry. [ABSTRACT FROM AUTHOR]

The previous studies have indicated that Photobacterium damselae subsp. damselae (Pdd) was the pathogen of black rockfish (Sebastes schlegeli) with seriously skin ulcer symptom. This study aimed to explore the spleen transcriptome response of S. schlegeli at 24 h (P24 group) and 48 h (P48 group) after Pdd infection and characterize expression profile of immune‐related genes. The fish in the control group were injected with equal volume of PBS. Results showed that there were 2,139 (88.42%), 510 (21.08%) and 242 (10%) differentially expressed genes in PBS vs P24, PBS vs P48 and P24 vs P48 respectively. As the time increases, the number of differential genes gradually decreases. GO annotation indicated that the immune‐related function category contributed the most in the PBS vs P24 and PBS vs P48 groups, including immune response, immune system process, immune effector process and regulation of immune system process. KEGG enrichment analysis showed that these genes were located on 277, 184 and 164 signalling pathways in the PBS vs P24, PBS vs P48 and P24 vs P48 groups respectively; among them, 30, 26 and 16 pathways were related to immune system, involving 344, 119 and 24 genes. P24 group involved more immune‐related signal pathways and genes than P48 group. RT‐qPCR validation indicated that the expression patterns of 10 genes at different time points were well agreed with RNA‐Seq analysis. This study provided a better understanding of the molecular responses to photobacteriosis in S. schlegeli. [ABSTRACT FROM AUTHOR]

Various bacteria that adhere to the gut are important for the health of fish. Regulating the microbial community in a desirable direction may be beneficial in aquaculture for preventing and controlling the diseases caused by pathogenic microbes. In this study, we investigated the changes in the microflora in the intestinal tracts of turbot (Scophthalmus maximus) larvae after introducing a probiotic (Bacillus amyloliquefaciens) after the first feed. B. amyloliquefaciens was added as part of a nutrient enrichment system in live feed (Branchionus plicatilis or Artemia sinica), so it passed into the intestinal tracts of the newly hatched turbot larvae. The turbot larvae were fed on live feed containing B. amyloliquefaciens in the experimental group, whereas live feed without the probiotic was provided to larvae in the control group. The total bacterial genomic DNA in the larval guts was extracted and sequenced with an Illumina HiSeq PE250 system. According to the sequencing results, the abundances of microbial species and the microflora diversity were lower in the intestines in the experimental group than the control. Throughout development, the microflora structure in the intestines was mainly constructed before the first feed and the composition of the dominant operational taxonomic units (OTUs) was stable, where the abundances of OTU8, OTU124, OTU150, OTU107, and OTU17 were always high. Compared with the control, the structures of the microflora in the intestines were similar on different days during the development and the growth of larvae in the experimental group. However, the similarity of the microflora structure between different treatments was low on the same day. Furthermore, the mean proportion of common OTUs was only 74.7% in different treatments on each day, which indicates that the introduction of B. amyloliquefaciens in the live feed changed the microflora structure in the intestine. During the early development stage (days 3–30), the average abundance of Pseudomonas was reduced by 0.8% whereas that of Lactococcus increased by 3.5% in the experimental group. Pseudomonas spp. are considered potentially pathogenic bacteria but there is no direct evidence for the pathogenicity of Lactococcus in turbot. Moreover, several Lactococcus species are regarded as probiotics in aquaculture. Therefore, the use of B. amyloliquefaciens could be beneficial for optimizing the microbial community structure in the intestines of turbot larvae, which may explain the probiotic effect of B. amyloliquefaciens. This study provides a theoretical basis for the biological regulation of the microflora structure in the intestinal tract during turbot breeding. [ABSTRACT FROM AUTHOR]

Photobacterium damselae subsp. damselae (PDD) is a Gram-negative bacterium that can infect a variety of aquatic organisms and humans. Based on an epidemiological investigation conducted over the past 3 years, PDD is one of the most important pathogens causing septic skin ulcer in deep-sea cage-cultured Sebastes schlegelii in the Huang-Bohai Sea area and present throughout the year with high abundance. To further understand the pathogenicity of this species, the pathogenic properties and genome of PDD strain SSPD1601 were analyzed. The results revealed that PDD strain SSPD1601 is a rod-shaped cell with a single polar flagellum, and the clinical symptoms were replicated during artificial infection. The SSPD1601 genome consists of two chromosomes and two plasmids, totaling 4,252,294 bp with 3,751 coding sequences (CDSs), 196 tRNA genes, and 47 rRNA genes. Common virulence factors including flagellin, Fur, RstB, hcpA, OMPs, htpB-Hsp60, VasK, and vgrG were found in strain SSPD1601. Furthermore, SSPD1601 is a pPHDD1-negative strain containing the hemolysin gene hlyAch and three putative hemolysins (emrA, yoaF, and VPA0226), which are likely responsible for the pathogenicity of SSPD1601. The phylogenetic analysis revealed SSPD1601 to be most closely related to Phdp Wu-1. In addition, the antibiotic resistance phenotype indicated that SSPD1601 was not sensitive to ceftazidime, pipemidic, streptomycin, cefalexin, bacitracin, cefoperazone sodium, acetylspiramycin, clarithromycin, amikacin, gentamycin, kanamycin, oxacillin, ampicillin, and trimethoprim-sulfamethoxazole, but only the bacitracin resistance gene bacA was detected based on Antibiotic Resistance Genes Database. These results expand our understanding of PDD, setting the stage for further studies of its pathogenesis and disease prevention. [ABSTRACT FROM AUTHOR]

One complete mitochondrial genomes (mitogenomes) was determined for Heterochaerus australis (Acoela, Convolutidae). Its mitochondrial genome size was 13,885 bp. The sequence contains 2 ribosomal RNA genes (rrnL and rrnS), 20 tRNA genes, and 12 protein-coding genes (PCGs). The A + T content of the complete mitochondrial genome sequence was 70.8%. The base composition showed a tendency of high AT. The resulted maximum likelihood (ML) tree supported that Acoela had a distant relationship with other orders of Turbellaria and the Xenacoelomorpha. [ABSTRACT FROM AUTHOR]

Forty-four microsatellite DNA markers were developed for silver carp, and used to investigate polymorphisms of 41 wild silver carps and seven wild bighead carps collected from Jingzhou fragment of Yangtze River. In silver carp, 40 markers were polymorphic. A total of 297 alleles were detected at 40 polymorphic loci. The number of alleles per locus varied from two to 16 with an average of 7.4 and the expected heterozygosities of each locus ranged from 0.07 to 0.91 with an average of 0.69. All markers amplified both silver carp and bighead carp DNAs. [ABSTRACT FROM AUTHOR]

Abstract: Complementary DNA (cDNA) sequences of Japanese seabass (Lateolabrax japonicus) and Japanese flounder (Paralichthys olivaceus) prion protein (PrP) encoding genes were cloned and characterized through RT-PCR approach. The PrPs of two fish species consist of 507 and 497 amino acid residues with an estimated molecular weight of about 54 and 52 kilodaltons, respectively. The deduced amino acid sequences of two sequences are about 65% similar to those of Japanese pufferfish (Fugu rubripes, stPrP-1) and Atlantic salmon (Salmo salar) in average, and bear the structural features of PrPs including a signal sequence, tandem repeats, a hydrophobic region, glycosylation sites, two cystein residues potentially involved in the formation of a disulphide bridge and a glycosyl phosphatidylinositol anchor site. The isolation of two PrP encoding genes will facilitate the exploration concerning the evolution, structure and function of PrPs and possible transmissible spongiform encephalopathies (TSE) in fish. [Copyright &y& Elsevier]

• The improvement of the rheological properties of asphalt by graphene was studied. • Using multiple-scale experiments combined with molecular dynamics simulation. • The focus is on the size effect of graphene on the modification efficiency. The use of waste rubber powder modified asphalt (RA) in road engineering can lead to environmental and economic benefits. However, there are still some concerns over the performance of the pavement with RA, especially the rheological properties under heavy traffic conditions. This paper aims to investigate the improvement effects of graphene on the rheological properties of RA using multiple-scale experimental characterizations combined with molecular dynamics simulation. Special attention was paid to the influence of geometric characteristics of graphene on the modification efficiency. The experimental findings demonstrated that the physical blending of graphene and RA could enhance viscoelasticity, persistent deformation, and mobility resistance of modified asphalt, while its low-temperature performances were marginally improved with the graphene. Graphene with a single layer or a few layers was more efficient in enhancing the high-temperature deformation and rutting resistance and microstructures of RA than that with multiple layers. The molecular dynamics simulation results showed that graphene could improve the shear viscosity of the modified asphalt and inhibit the diffusion of asphalt components, and the effect on the low-temperature performance is related to the size effect. Moreover, the size of graphene particles could strongly influence the performances of the modified asphalt. Specifically, increasing the graphene size decreased the shear viscosity, free volume fraction, and glass transition temperature, indicating the improved deformation resistance. The change in the number of graphene layers was more effective in altering the modification effect of small-sized graphene compared to large-sized graphene. This research can offer a theoretical guideline for optimizing the use of graphene in modified asphalt. [ABSTRACT FROM AUTHOR]

MicroRNAs, as one of the post-transcriptional regulation of genes, play an important role in the development process, cell differentiation and immune defense. The sea cucumber Apostichopus japonicus is an important cold-water species, known for its excellent nutritional and economic value, which usually encounters heat stress that affects its growth and leads to significant economic losses. However, there are few studies about the effect of miRNAs on heat stress in sea cucumbers. In this study, high-throughput sequencing was used to analyze miRNA expression in the body wall of sea cucumber between the control group (CS) and the heat stress group (HS). A total of 403 known miRNAs and 75 novel miRNAs were identified, of which 13 miRNAs were identified as significantly differentially expressed miRNAs (DEMs) in response to heat stress. A total of 16,563 target genes of DEMs were predicted, and 101 inversely correlated target genes that were potentially regulated by miRNAs in response to heat stress of sea cucumbers were obtained. Based on these results, miRNA-mRNA regulatory networks were constructed. The expression results of high-throughput sequencing were validated in nine DEMs and four differentially expressed genes (DEGs) by quantitative real-time polymerase chain reaction (RT-qPCR). Moreover, pathway enrichment of target genes suggested that several important regulatory pathways may play an important role in the heat stress process of sea cucumber, including ubiquitin-mediated proteolysis, notch single pathway and endocytosis. These results will provide basic data for future studies in miRNA regulation and molecular adaptive mechanisms of sea cucumbers under heat stress., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Chang, Li, Liao, Rong, Wang, Wang, Yu, Zhang and Wang.)

Increasing discoveries of new species of the genus Melanochlamys Cheeseman, 1881 in the recent years indicate that the biodiversity of this group remains underestimated. Recently, several aglajid sea slugs were collected from Laizhou Bay, Shandong Province, China. Morphological observation of their external and internal anatomy revealed that they represent an undescribed species of Melanochlamys. This new species, Melanochlamys aquilina sp. nov., is closely related to Melanochlamys fukudai Cooke, Hanson, Hirano, Ornelas-Gatdula, Gosliner, Chernyshev Valdés, 2014 in body size and dark external coloration, but can be differentiated from the latter by features of both shell and male reproductive organ. Phylogenetic analyses of two mitochondrial (COI, 16S rRNA) and a nuclear (H3) genes using Bayesian inference, maximum likelihood, and species delimitation analysis also support the separation of Melanochlamys aquilina sp. nov. from its related congeners.

One complete mitochondrial genome (mitogenome) was determined for a deep-sea holothurian species of the genus Synallactes (Synallactida: Synallactidae). The mitochondrial genome size of the sea cucumber was 15,920 bp. The sequence contains 2 ribosomal RNA genes (12S and 16S), 22 transfer RNA genes, and 13 protein-coding genes, as found in most previously determined holothurian mitogenomes. The A + T content of the complete mitochondrial genome sequence was 64.45%. The base composition showed a tendency of AT. The resulted maximum likelihood (ML) tree of Holothuroidea supported that Synallactes sp. is a species of Synallactida., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Vibrio splendidus is identified as one of the major pathogenic factors for the skin ulceration syndrome in sea cucumber (Apostichopus japonicus), which has vastly limited the development of the sea cucumber culture industry. In order to screen the immune genes involving Vibrio splendidus challenge in sea cucumber and explore the molecular mechanism of this process, the related transcriptome and gene expression profiling of resistant and susceptible biotypes of sea cucumber with Vibrio splendidus challenge were collected for analysis. A total of 319,455,942 trimmed reads were obtained, which were assembled into 186,658 contigs. After that, 89,891 representative contigs (without isoform) were clustered. The analysis of the gene expression profiling identified 358 differentially expression genes (DEGs) in the bacterial-resistant group, and 102 DEGs in the bacterial-susceptible group, compared with that in control group. According to the reported references and annotation information from BLAST, GO and KEGG, 30 putative bacterial-resistant genes and 19 putative bacterial-susceptible genes were identified from DEGs. The qRT-PCR results were consistent with the RNA-Seq results. Furthermore, many DGEs were involved in immune signaling related pathways, such as Endocytosis, Lysosome, MAPK, Chemokine and the ERBB signaling pathway.

Twenty microsatellite DNA markers were developed for sea cucumber and used to investigate polymorphisms of 60 wild Apostichopus japonicus individuals collected from China. It revealed that all the markers were polymorphic. A total of 164 alleles were detected at 20 loci. The number of alleles per locus varied from 3 to 17 with an average of 8.2, and the expected heterozygosities of each locus ranged from 0.03 to 0.89 with an average of 0.64. Cross-species amplification was also conducted in Parastichopus parvimensis collected from the United States and Pathallus mollis collected from Peru. The result showed that 17 loci amplified Parastichopus parvimensis DNAs while only 4 loci could amplify Pathallus mollis DNAs. All of the polymorphic markers would be useful for future genetic breeding and the assessment of genetic variation within sea cucumbers.