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Sulfidogenic and methanogenic processes are undesirable in sewer management, yet the derived problems regarding organic losses are often neglected. Traditional chemical dosing methods aimed at sulfide and methane control commonly involve similar mechanisms of oxidation and/or precipitation. Moreover, previous focuses were centered on elevating control efficacy rather than investigating interactions between dosed chemicals and biofilms. In this work, organic silicon quaternary ammonium salt (QSA) of 75 mg-N/L was firstly applied in laboratory pressurized sewer reactors. After three dosing events, it took 20 days for sulfidogenic activities to recover to 50 % without further elevations. Meantime, methanogenic activities were stable ca. 11 % without significant inclinations to recover. Notably, consumption rate of chemical oxygen demand (COD) was suppressed to 50 % at most, and no microbial resistance to QSA but better control efficacy was observed. Characterizations of physicochemistry, microbial community and metabolism were conducted to elucidate mechanisms. Results showed that QSA was attached on sewer biofilms via electrostatic attraction to exert enduring control efficacy. Biofilms tended to become more hydrophobic and compact after QSA exposure. Microbial analyses indicated that relative abundances of microbes regarding hydrolysis, acidogenesis and methanogenesis were sharply decreased together with down-regulation of pivotal enzymatic activities. Additionally, denitrification batch tests initially suggested that the biodegradability of effluent was significantly enhanced, which ensured the safety of QSA dosing into sewers. Overall, results of this work were expected to lay a theoretical foundation on employing QSA to wastewater management.

Peracetic acid (PAA), known for its environmentally friendly properties as a oxidant and bactericide, is gaining prominence in decontamination and disinfection applications. The primary product of PAA oxidation is acetate that can serve as an electron acceptor (EA) for the biosynthesis of medium-chain fatty acids (MCFAs) via chain elongation (CE) reactions. Hence, PAA-based pretreatment is supposed to be beneficial for MCFAs production from anaerobic sludge fermentation, as it could enhance organic matter availability, suppress competing microorganisms and furnish EA by providing acetate. However, such a hypothesis has rarely been proved. Here we reveal that PAA-based pretreatment leads to significant exfoliation of extracellular polymeric substances (EPS) from sludge flocs and disruption of proteinic secondary structures, through inducing highly active free radicals and singlet oxygen. The production of MCFAs increases substantially to 11,265.6 mg COD L−1, while the undesired byproducts, specifically long-chain alcohols (LCAs), decrease to 723.5 mg COD L−1. Microbial activity tests further demonstrate that PAA pretreatment stimulates the CE process, attributed to the up-regulation of functional genes involved in fatty acid biosynthesis pathway. These comprehensive findings provide insights into the effectiveness and mechanisms behind enhanced MCFAs production through PAA-based technology, advancing our understanding of sustainable resource recovery from sewage sludge.

Japanese flounder is usually gonochoristic, with gonads that are either testes or ovaries. Here, we report an unusual case of hermaphroditism in Japanese flounder captured from the Bohai Sea. In the intersex flounder, the membrane of the upper ovary was closely connected to the abdominal muscles and internal organs, and the eggs filled the entire abdomen. The lower ovary was small and closely connected to the testes. The testes contained few fully mature sperm. Both eggs and sperm were capable of fertilization. The levels of several reproduction-related hormones (17β-estradiol, 11-ketotestosterone, 17α, 20β-dihydroxyprogesterone, luteinizing hormone, follicle-stimulating hormone, and testosterone) in the intersex flounder were intermediate, between those in females and males. The results showed that the heterozygosity of the intersex flounder was 0.632, and there were 28 single-nucleotide polymorphisms in the cyp21a gene. Compared with that of wild flounder, the activity of 21-hydroxylase was reduced by approximately 20.0%, and expressions of cyp19a, amh, and dmrt1 differed. We present the first report of its kind, detailing the anatomy, hormonal endocrinology, molecular biology, and physiology of the intersex Japanese flounder.

Since the advent of germ cell transplantation (GCT), it has been widely used in shortening the fish breeding cycle, sex-controlled breeding and the protection of rare and endangered fish. In this study, the effectiveness of female sterile recipient preparation and donor stem cell isolation and purification were comprehensively evaluated for spermatogonial stem cell transplantation (SSCT) in Paralichthys olivaceus. The best way to prepare sterile recipients was found to be giving three-year-old fish four intraovarian injections of busulfan (20 mg/kg body weight) combined with exposure to a high temperature (28 °C) after the spawning season compared with the two other ways, which induced apoptosis of most of the endogenous germ cells, resulting in shrinkage of the spawning plate and enlargement of the ovarian lumen. Further analysis showed that both the gonadosomatic index and germ-cell-specific vasa expression were significantly lower than those of the natural-temperature group before treatment (p < 0.05). A high percentage (>60.00%) of spermatogonial stem cells (SSCs) were obtained after isolation and purification and were transplanted into the prepared recipients. After three weeks of SSCT, the numbers of PKH26-labeled SSCs were increased in the ovaries of the recipients. These findings provide a basis for the establishment of an ideal SSCT technique using P. olivaceus females as the recipients, ultimately contributing to the efficient conservation of male germplasm resources and effective breeding.

IntroductionVibriosis causes enormous economic losses of marine fish. The present study investigated the intestinal microbial response to acute infection of half-smooth tongue sole with different-dose Vibrio alginolyticus within 72 h by metagenomic sequencing.MethodsThe inoculation amount of V. alginolyticus for the control, low-dose, moderate-dose, and high-dose groups were 0, 8.5 × 101, 8.5 × 104, and 8.5 × 107 cells/g respectively, the infected fish were farmed in an automatic seawater circulation system under a relatively stable temperature, dissolved oxygen and photoperiod, and 3 ~ 6 intestinal samples per group with high-quality DNA assay were used for metagenomics analysis.ResultsThe acute infections with V. alginolyticus at high, medium, and low doses caused the change of different-type leukocytes at 24 h, whereas the joint action of monocytes and neutrophils to cope with the pathogen infection only occurred in the high-dose group at 72 h. The metagenomic results suggest that a high-dose V. alginolyticus infection can significantly alter the intestinal microbiota, decrease the microbial α-diversity, and increase the bacteria from Vibrio and Shewanella, including various potential pathogens at 24 h. High-abundance species of potential pathogens such as V. harveyii, V. parahaemolyticus, V. cholerae, V. vulnificus, and V. scophthalmi exhibited significant positive correlations with V. alginolyticus. The function analysis revealed that the high-dose inflection group could increase the genes closely related to pathogen infection, involved in cell motility, cell wall/ membrane/envelope biogenesis, material transport and metabolism, and the pathways of quorum sensing, biofilm formation, flagellar assembly, bacterial chemotaxis, virulence factors and antibiotic resistances mainly from Vibrios within 72 h.DiscussionIt indicates that the half-smooth tongue sole is highly likely to be a secondary infection with intestinal potential pathogens, especially species from Vibrio and that the disease could become even more complicated because of the accumulation and transfer of antibiotic-resistance genes in intestinal bacteria during the process of V. alginolyticus intensified infection.

The roughskin sculpin (Trachidermus fasciatus) is an endangered fish species in China. In recent years, artificial breeding technology has made significant progress, and the population of roughskin sculpin has recovered in the natural environment through enhancement programs and the release of juveniles. However, the effects of released roughskin sculpin on the genetic structure and diversity of wild populations remain unclear. Studies on genetic diversity analysis based on different types and numbers of molecular markers have yielded inconsistent results. In this study, we obtained 2,610,157 high-quality SNPs and 494,698 InDels through whole-genome resequencing of two farmed populations and one wild population. Both farmed populations showed consistent levels of genomic polymorphism and a slight increase in linkage compared with wild populations. The population structure of the two farmed populations was distinct from that of the wild population, but the degree of genetic differentiation was low (overall average Fst = 0.015). Selective sweep analysis showed that 523,529 genes were selected in the two farmed populations, and KEGG enrichment analysis showed that the selected genes were related to amino acid metabolism, which might be caused by artificial feeding. The findings of this study provide valuable additions to the existing genomic resources to help conserve roughskin sculpin populations.

Abstract Breast cancer cells with stem-like properties are critical for tumor progression, yet much about these cells remains unknown. Here, we characterize a population of stem-like breast cancer cells expressing the integrin αvβ3 as transcriptionally related to activated stem/basal cells in the normal human mammary gland. An unbiased functional screen of genes unique to these cells identified the matrix protein TGFBI (BIG-H3) and the transcription factor ZEB1 as necessary for tumorsphere formation. Surprisingly, these genes were not required for cell proliferation or survival, but instead maintained chromosomal stability. Consistent with this finding, CRISPR deletion of either gene synergized with PARP inhibition to deplete αvβ3+ stem-like cells, which are normally resistant to this therapy. Our findings highlight a critical role for TGFBI-ZEB1 protection against genetic stress as a key attribute of activated stem-like cells and suggest that disrupting this ability may enhance their “BRCAness” by increasing sensitivity to PARP inhibitors.

The potential of periodate (PI) in sludge anaerobic digestion is not tapped, although it has recently attracted great research interest in organic contaminants removal and pathogens inactivation in wastewater treatment. This is the first work to demonstrate significant improvement in methane generation from waste activated sludge (WAS) with PI pretreatment and to provide underlying mechanisms. Biochemical methane potential tests indicated that methane yield enhanced from 100.2 to 146.3 L per kg VS (VS, volatile solids) with PI dosages from 0 to 100 mg per g TS (TS, total solids). Electron spin resonance showed PI could be activated without extra activator addition, which might be attributed to the native transition metals (e.g., Fe2+) in WAS, thereby generating hydroxyl radical (•OH), superoxide radicals (•O2−), and singlet oxygen (1O2). Further scavenging tests demonstrated all of them synergistically promoted WAS disintegration, and their contributions were in the order of •O2− > •OH > 1O2, leading to the release of substantial biodegradable substances (i.e., proteins and polysaccharides) into the liquid phase for subsequent biotransformation. Moreover, fluorescence and ultraviolet spectroscopy analyses indicated the recalcitrant organics (especially lignocellulose and humus) could be degraded by reducing their aromaticity under oxidative stress of PI, thus readily for methanogenesis. Microbial community analysis revealed some microorganisms participating in hydrolysis, acidogenesis, and acetoclastic methanogenesis were enriched after PI pretreatment. The improved key enzyme activities and up-regulated metabolic pathways further provided direct evidence for enhanced methane production. This research was expected to broaden the application scope of PI and provide more diverse pretreatment choices for energy recovery through anaerobic digestion.

Abstract Background Tissue heterogeneity significantly influences the overall saccharification efficiency of plant biomass. However, the mechanisms of specific organ or tissue recalcitrance to enzymatic deconstruction are generally complicated and unclear. A multidimensional analysis of the anatomical fraction from 12 corn cultivars was conducted to understand the essence of recalcitrance. Results The results showed that leaf, leaf sheath, stem pith and stem rind of corn straw exhibited remarkable heterogeneity in chemical composition, physical structure and cell type, which resulted in the different saccharification ratio of cellulose. The high saccharification ratio ranging from 21.47 to 38.96% was in stem pith, whereas the low saccharification ratio ranging from 17.1 to 27.43% was in leaf sheath. High values of lignin, hemicelluloses, degree of polymerization and crystallinity index were critical for the increased recalcitrance, while high value of neutral detergent soluble and pore size generated weak recalcitrance. Interestingly, pore traits of cell wall, especial for microcosmic interface structure, seemed to be a crucial factor that correlated to cellulase adsorption and further affected saccharification. Conclusions Highly heterogeneity in cell wall traits influenced the overall saccharification efficiency of biomass. Furthermore, the holistic outlook of cell wall interface was indispensable to understand the recalcitrance and promote the biomass conversion. Graphic abstract

Background and objective: Urolithiasis or renal stones form a major urinary tract infection with formation of calcifications in the bladder and uterus. With the lifestyle diseases burgeoning, the renal stones have become a common cause with an approximate 1 in 1000 people affected all over the world with a risk ratio of 3 : 1 in men and women. On the other hand, prostate or genitourinary cancers are well documented to be associated with urolithiasis. Methods: A gene list was prepared from the published NCBI dataset, comprising all the genes related to urolithiasis primarily with mutations (both pathogenic and likely pathogenic Single nucleotide polymorphisms, SNP’s) for every particular gene screened later from the published datasets. To see the interactions among all the potential genetic factors, PPI based tools were used and an interaction map was prepared. For the characterization of mutations, we have used gnomAD for verifying all the SNPs whether they are synonymous or nonsynonymous mutations. Results: We outlined the list of genes and discussed the systems bioinformatics integrated approach associated with it. Conclusion: We found a large number of genes common to them and their association is subtly known for immunomodulatory response.

Scutellaria baicalensis Georgi. (Chinese skullcap or Huang-qin) is an extremely crucial medicinal plant in the Labiate family, and the color of its flowers naturally appears purple. However, during the long-term cultivation of S. baicalensis, very few plants of S. baicalensis also present white and purple-red flower colors under the same ecological conditions. However, the complex metabolic and transcriptional networks underlying color formation in white, purple-red, and purple flowers of S. baicalensis remain largely unclarified. To gain an insight into this issue, we conducted transcriptome and metabolomic profiling to elucidate the anthocyanin synthesis metabolic pathway in the flowers of S. baicalensis, and to identify the differentially expressed candidate genes potentially involved in the biosynthesis of anthocyanins. The results showed that 15 anthocyanins were identified, among which cyanidin 3-rutinoside and delphin chloride were the primary anthocyanins, and accumulation was significantly related to the flower color changes of S. baicalensis. Furthermore, the down-regulation of SbDFR (Sb02g31040) reduced the anthocyanin levels in the flowers of S. baicalensis. The differential expression of the Sb3GT (Sb07g04780 and Sb01g72290) gene in purple and purple-red flowers affected anthocyanin accumulation, suggesting that anthocyanin levels were closely associated with the expression of SbDFR and Sb3GT, which play important roles in regulating the anthocyanin biosynthesis process of S. baicalensis flowers. Transcriptomic analysis revealed that transcription factors WRKY, bHLH, and NAC were also highly correlated with anthocyanin accumulation, especially for NAC35, which positively regulated SbDFR (Sb02g31040) gene expression and modulated anthocyanin biosynthesis in flower color variation of S. baicalensis. Overall, this study presents the first experimental evidence for the metabolomic and transcriptomic profiles of S. baicalensis in response to flower coloration, which provides a foundation for dynamic metabolic engineering and plant breeding, and to understand floral evolution in S. baicalensis plants.

A new cell line Japanese flounder spleen (JFSP) derived from the spleen of Japanese flounder (Paralichthys olivaceus) was established and characterized in this study. The JFSP cells grew rapidly at 29 °C, and the optimum fetal bovine serum concentration in the L-15 medium was 15%. Cells were subcultured for more than 80 passages. The JFSP cells have a diploid chromosome number of 2n = 68, which differs from the chromosome number of normal diploid Japanese flounder. The established cells were susceptible to Bohle virus (BIV), Viral hemorrhagic septicemia virus (VHSV), Hirame rhabdovirus (HIRRV), Infectious hematopoietic necrosis virus (IHNV), and Lymphocystis disease virus (LCDV), as evidenced by varying degrees of cytopathic effects (CPE). Replication of the virus in JFSP cells was confirmed by qRT-PCR and transmission electron microscopy. In addition, the expression of four immune-related genes, TRAF3, IL-1β, TNF-α, and TLR2, was differentially altered following viral infection. The results indicated that the cells underwent an antiviral immune response. JFSP cell line is an ideal tool in vitro for virology. The use of fish cell lines to study the immune genes and immune mechanism of fish and to clarify the immune mechanism of fish has important theoretical significance and practical application value for the fundamental prevention and treatment of fish diseases.

Localization of the underwater magnetic sensor arrays plays a pivotal role in the magnetic silencing facility. A localization approach is proposed for underwater sensors based on the optimization of magnetic field gradients in the inverse problem of localization. In the localization system, a solenoid coil carrying direct current serves as the magnetic source. By measuring the magnetic field generated by the magnetic source in different positions, an objective function is established. The position vector of the sensor is determined by a novel multi-swarm particle swarm optimization with dynamic learning strategy. Without the optimization of the magnetic source’s positions, the sensors’ positions, especially in the z-axis direction, struggle to meet the requested localization. A strategy is proposed to optimize the positions of the magnetic source based on magnetic field gradients in the three directions of x, y and z axes. Compared with the former method, the model experiments show that the proposed method could achieve a 10 cm location error for the position type 2 sensor and meet the request of localization.

A novel nidovirus, CSBV Bces-Po19, was isolated from the marine fish, Japanese flounder (Paralichthys olivaceus). The viral genome was 26,597 nucleotides long and shared 98.62% nucleotide identity with CSBV WHQSR4345. PacBio Sequel and Illumina sequencing were used to perform full-length transcriptome sequencing on CSBV Bces-Po19-sensitive (S) and -resistant (R) Japanese flounder. The results of negative staining revealed bacilliform and spherical virions. There were in total 1444 different genes between CSBV Bces-Po19 S and R groups, with 935 being up-regulated and 513 being down-regulated. Metabolism-, immune-, and RNA-related pathways were significantly enriched. Furthermore, CSBV Bces-Po19 infection induced alternative splicing (AS) events in Japanese flounder; the S group had a higher numbers of AS events (12,352) than the R group (11,452). The number of long non-coding RNA (lncRNA) in the S group, on the other hand, was significantly lower than in the R group. In addition to providing valuable information that sheds more light on CSBV Bces-Po19 infection, these research findings provide further clues for CSBV Bces-Po19 prevention and treatment.

The liver can synthesize vitellogenin, the precursor of vitellin, which is needed for oocyte development and maturation. Here, we investigated the effects of infertility on liver structure, hormone regulation, and gene and protein networks in Japanese flounder (Paralichthys olivaceus). Results showed that the liver of infertile fish had fewer vacuoles and significantly lower serum vitellogenin (VTG) level than in liver of fertile fish. Whole transcriptomics analysis between infertile and fertile groups identified 2076 significantly differentially expressed (DE) mRNAs, 431 DE lncRNAs, 265 DE circRNAs, and 53 DE miRNAs. Proteomics analysis identified 838 DE proteins. Integrated analysis of whole transcriptomics and proteomics revealed 60 significantly DE genes and proteins associated with metabolism, immunity, signal transduction, and steroid biosynthesis. Moreover, non-coding RNA (miRNAs, circRNA, and lncRNA) transcripts involved in metabolism, immunity, and signal transduction in infertile liver were identified. In conclusion, this study shows that gonadal infertility is associated with not only changes in histological structure and hormone secretion but also changes in metabolism, immunity, and signal transduction networks in the liver. These results provide valuable information concerning the mechanism underlying infertility in fish.

Sterility is a serious problem that can affect all bionts. In teleosts, double haploids (DHs) induced by mitogynogenesis are often sterile. This sterility severely restricts the further application of DHs for production of clones, genetic analysis, and breeding. However, sterile DH individuals are good source materials for investigation of the molecular mechanisms of gonad development, especially for studies into the role of genes that are indispensable for fish reproduction. Here, we used the Illumina sequencing platform to analyze the transcriptome of sterile female DH Japanese flounder in order to identify major genes that cause sterility and to provide a molecular basis for an intensive study of gonadal development in teleosts. Through sequencing, assembly, and annotation, we obtained 52,474 contigs and found that 60.7% of these shared homologies with existing sequences. A total of 1225 differentially expressed unigenes were found, including 492 upregulated and 733 downregulated genes. Gene Ontology and KEGG analyses showed that genes showing significant upregulation, such as CYP11A1, CYP11B2, CYP17, CYP21, HSD3β, bcl2l1, and PRLR, principally correlated with sterol metabolic process, steroid biosynthetic process, and the Jak-stat signaling pathway. The significantly downregulated genes were primarily associated with immune response, antigen processing and presentation, cytokine-cytokine receptor interaction, and protein digestion and absorption. Using a co-expression network analysis, we conducted a comprehensive comparison of gene expression in the gonads of fertile and sterile female DH Japanese flounder. Identification of genes showing significantly different expression will provide further insights into DH reproductive dysfunction and oocyte maturation processes in teleosts.

The incidence of colorectal cancer (CRC) has been increasing in recent years. Thus, the discovery of factors that can assist in alleviating CRC is urgently warranted. Methods: To identify a potential factor involved in the development of CRC, we screened the upregulated genes in tumor tissues through four datasets from an online database. The expression of reticulocalbin 1 (RCN1), a Ca2+-binding protein, was upregulated in the four datasets. Based on loss-offunction experiments, the effect of RCN1 on cell viability was assessed by Cell Counting Kit-8 (CCK-8) assay. The regulatory effect of RCN1 on apoptosis was evaluated through Annexin V-fluorescein 5-isothiocyanate (FITC)/propidium iodide (PI) staining assay and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assay in RKO and SW480 cells. Activation of endoplasmic reticulum (ER) stress signaling pathways was confirmed by estimating the phosphorylation and expression of PRKR-like ER kinase (PERK), inositol-requiring kinase-1 (IRE1), transcription factor 6 (ACT6), and CCAAT/enhancer-binding protein-homologous protein (CHOP). The intracellular Ca2+ homeostasis regulated by RCN1 was determined through the detection of Ca2+ concentration and mitochondrial membrane potential (MMP) measurement. Moreover, whether inositol 1,4,5-trisphosphate receptor type 1 (IP3R1) was involved in the regulation of RCN1 in CRC was verified through the depletion of IP3R1 in RKO cells. Results: Knockdown of RCN1 reduced cell viability and facilitated apoptosis in RKO and SW480 cells. Phosphorylation of PERK and IRE1, activation of ATF6, and upregulation of CHOP were induced by the absence of RCN1, suggesting that the unfolded protein response (UPR) was activated in CRC cells. The concentration of Ca2+ in mitochondria was increased after RCN1 depletion, followed by reduction in the MMP and release of cytochrome c from mitochondria to the cytoplasm in RKO and SW480 cells. Moreover, it was demonstrated that IP3R1 mediates the effect of RCN1 on apoptosis induced by ER stress in CRC cells. The downregulation of IP3R1 restored the RCN1 loss-induced apoptosis and the increased Ca2+ concentration. Conclusion: Taken together, our results confirmed that silencing of RCN1 disrupted intracellular Ca2+ homeostasis and promoted cell apoptosis caused by TG-induced ER stress by regulating IP3R1 and activating the UPR signaling pathways. [ABSTRACT FROM AUTHOR]