FishSNP: a high quality cross-species SNP database of fishes.

The progress of aquaculture heavily depends on the efficient utilization of diverse genetic resources to enhance production efficiency and maximize profitability. Single nucleotide polymorphisms (SNPs) have been widely used in the study of aquaculture genomics, genetics, and breeding research since they are the most prevalent molecular markers on the genome. Currently, a large number of SNP markers from cultured fish species are scattered in individual studies, making querying complicated and data reuse problematic. We compiled relevant SNP data from literature and public databases to create a fish SNP database, FishSNP ( http://bioinfo.ihb.ac.cn/fishsnp ), and also used a unified analysis pipeline to process raw data that the author of the literature did not perform SNP calling on to obtain SNPs with high reliability. This database presently contains 45,690,243 (45 million) nonredundant SNP data for 13 fish species, with 30,288,958 (30 million) of those being high-quality SNPs. The main function of FishSNP is to search, browse, annotate and download SNPs, which provide researchers various and comprehensive associated information.

Knowledge, attitude, and practice toward photoaging in the Chinese population: a cross-sectional study.

To investigate the knowledge, attitude, and practice (KAP) of photoaging in the Chinese population. This web-based cross-sectional study was conducted between January 2023 and March 2023 among the Chinese population aged 18-80 years old. Participants' knowledge, attitude, and practice toward photoaging were collected through a self-administered questionnaire. A total of 830 questionnaires were collected, with 826 valid questionnaires and an efficiency rate of 99.52%. There were 274 (33.17%) males and 532 (64.41%) aged 31-51 years old. The average knowledge, attitude, and practice scores were 7 (4, 9) (possible range 0-12), 31.5 (28, 34) (possible range 8-40), and 33 (24, 42) (possible range 11-55), respectively, indicating poor knowledge, good attitude, and moderate practice. Spearman correlation analysis showed that knowledge was negatively correlated with attitude (r = - 0.111, P < 0.05) and practice (r = - 0.113, P < 0.05), and attitude was positively correlated with practice (r = 0.992, P < 0.05). The multivariable linear regression model showed that for each point increase in attitude score, the practice score increased by 2.96 points (ß = 2.96, 95% CI 2.91-3.01, P < 0.001). The Chinese population has poor knowledge, good attitude, and moderate practice toward photoaging. A good attitude toward photoaging would lead to good practice, and more outreach and education for the Chinese population might be needed.

PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping.

Parentage assignment is a genetic test that utilizes genetic characteristics, such as molecular markers, to identify the parental relationships within populations, which, in commercial fish farming, are almost always large and where full information on potential parents is known. To accurately find the true parents, the genotypes of all loci in the parentage marker set (PMS) are required for each individual being tested. With the same accuracy, a PMS containing a smaller number of markers will undoubtedly save experimental costs. Thus, this study established a scheme to screen low-redundancy PMSs using the exhaustive algorithm and greedy algorithm. When screening PMSs, the greedy algorithm selects markers based on the parental dispersity index (PDI), a uniquely defined metric that outperforms the probability of exclusion (PE). With the conjunctive use of the two algorithms, non-redundant PMSs were found for more than 99.7% of solvable cases in three groups of random sample experiments in this study. Then, a low-redundancy PMS can be composed using two or more of these non-redundant PMSs. This scheme effectively reduces the number of markers in PMSs, thus conserving human and experimental resources and laying the groundwork for the widespread implementation of parentage assignment technology in economic species breeding.

Allele-dependent expression and functionality of lipid enzyme phospholipid:diacylglycerol acyltransferase affect diatom carbon storage and growth.

In the acyl-CoA-independent pathway of triacylglycerol (TAG) synthesis unique to plants, fungi, and algae, TAG formation is catalyzed by the enzyme phospholipid:diacylglycerol acyltransferase (PDAT). The unique PDAT gene of the model diatom Phaeodactylum tricornutum strain CCMP2561 boasts 47 single nucleotide variants within protein coding regions of the alleles. To deepen our understanding of TAG synthesis, we observed the allele-specific expression of PDAT by the analysis of 87 published RNA-sequencing (RNA-seq) data and experimental validation. The transcription of one of the two PDAT alleles, Allele 2, could be specifically induced by decreasing nitrogen concentrations. Overexpression of Allele 2 in P. tricornutum substantially enhanced the accumulation of TAG by 44% to 74% under nutrient stress; however, overexpression of Allele 1 resulted in little increase of TAG accumulation. Interestingly, a more serious growth inhibition was observed in the PDAT Allele 1 overexpression strains compared with Allele 2 counterparts. Heterologous expression in yeast (Saccharomyces cerevisiae) showed that enzymes encoded by PDAT Allele 2 but not Allele 1 had TAG biosynthetic activity, and 7 N-terminal and 3 C-terminal amino acid variants between the 2 allele-encoded proteins substantially affected enzymatic activity. P. tricornutum PDAT, localized in the innermost chloroplast membrane, used monogalactosyldiacylglycerol and phosphatidylcholine as acyl donors as demonstrated by the increase of the 2 lipids in PDAT knockout lines, which indicated a common origin in evolution with green algal PDATs. Our study reveals unequal roles among allele-encoded PDATs in mediating carbon storage and growth in response to nitrogen stress and suggests an unsuspected strategy toward lipid and biomass improvement for biotechnological purposes.

Transcriptome analysis revealed the existence of family-specific regulation of growth traits in grass carp.

The grass carp (Ctenopharyngodon idella) is the world's most prolific freshwater fish. Little is known, however, about the functional genes and genetic regulatory networks that govern its growth traits. We created three grass carp families in this study by using two grass carp parents with fast-growing offspring and two grass carp parents with slow-growing offspring, namely the fast-growing × fast-growing family (FF), the slow-growing × slow-growing family (SS), and the fast-growing × slow-growing family (FS). Under the satiation and starvation feeding modes, the average body weight of these families' offspring exhibited a consistent ordering (FF > FS > SS). The transcriptomes of grass carp whole brain and hepatopancreas were then acquired for each family, and it was discovered that the number of differentially expressed genes (DEGs) in the different organs demonstrated family specificity. DEGs were mostly identified in the hepatopancreas of FF and the whole brain of SS, but they were more evenly distributed in FS. There were 14 DEGs that were found in all three families, including three that were negatively correlated in hepatopancreas (ahsg2, lect2) or in brain (drd5), and 11 that were positively connected in hepatopancreas (sycn, pabpc4, zgc:112294, cel, endou, ela2, prss3, zbtb41, ela3) or in brain (fabp7, endod1). The deletion of ahsg2 boosted the growth rate only in certain zebrafish, suggesting that the growth-promoting effects of ahsg2 varies among individuals. Furthermore, we examined the SNP in each family and conducted preliminary research on the probable genetic pathways of family-specific control of growth traits. The family specificity of the growth regulation mechanism of grass carp at the transcriptional level was revealed for the first time in this study, and it was discovered that growth differences among individuals in the FF family were primarily due to differences in nutrient metabolism, whereas growth differences among individuals in the SS family may be primarily due to differences in foraging ability caused by differences in brain development. This research adds to our understanding of the genetic regulatory mechanism of grass carp growth.

The manipulation of cell suspensions from zebrafish intestinal mucosa contributes to understanding enteritis.

Background: Although zebrafish are commonly used to study intestinal mucosal immunity, no dedicated procedure for isolating immune cells from zebrafish intestines is currently available. A speedy and simple operating approach for preparing cell suspension from mucosa has been devised to better understanding of intestinal cellular immunity in zebrafish. Methods and results: The mucosal villi were separated away from the muscle layer by repeated blows. The complete deprivation of mucosa was done and evidenced by HE and qPCR results. Higher expression of both innate (mpeg1, mpx, and lck) and adaptive immune genes (zap70, blnk, foxp3a, and foxp3b) was revealed compared to cells obtained by typical mesh rubbing. The cytometric results also revealed that the tested operation group had a higher concentration and viability. Further, fluorescent-labelled immune cells from 3mo Tg(lyz:DsRED2), Tg(mpeg1:EGFP), Tg(Rag2:DsRED), and Tg(lck:EGFP), were isolated and evaluated for the proportion, and immune cells' type could be inferred from the expression of marker genes. The transcriptomic data demonstrated that the intestinal immune cell suspension made using the new technique was enriched in immune-related genes and pathways, including il17a/f, il22, cd59, and zap70, as well as pattern recognition receptor signaling and cytokine-cytokine receptor interaction. In addition, the low expression of DEG for the adherent and close junctions indicated less muscular contamination. Also, lower expression of gel-forming mucus-associated genes in the mucosal cell suspension was consistent with the current less viscous cell suspension. To apply and validate the developed manipulation, enteritis was induced by soybean meal diet, and immune cell suspensions were analyzed by flow cytometry and qPCR. The finding that in enteritis samples, there was inflammatory increase of neutrophils and macrophages, was in line with upregulated cytokines (il8 and il10) and cell markers (mpeg1 and mpx). Conclusion: As a result, the current work created a realistic technique for studying intestinal immune cells in zebrafish. The immune cells acquired may aid in further research and knowledge of intestinal illness at the cellular level.

FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization.

With the rapid expansion of transcriptome studies in many fishes, a great number of RNA-seq data have been published, allowing for a more systematic understanding of the general profiles and details of gene expression in fish. FishGET is dedicated to gathering and curating fish RNA-seq data to discover more new RNAs, including mRNA and lncRNA, thereby getting a more complete reference transcriptome and providing more comprehensive and accurate transcriptome annotations. We obtained a total of 1362 RNA-seq paired-end data of 8 fishes from 97 different studies, and then we performed transcript assembly, meta-assembly, weighted gene co-expression network analysis (WGCNA), functional annotations, neighbor location annotation, lncRNA type annotation, homology annotation. To promote research into fish genes at the transcriptional level, we developed a user-friendly web interface that allows users to view all information and makes use of multiple types of dynamic interactive visualization services.

Transcriptomes of Zebrafish in Early Stages of Multiple Viral Invasions Reveal the Role of Sterols in Innate Immune Switch-On.

Although it is widely accepted that in the early stages of virus infection, fish pattern recognition receptors are the first to identify viruses and initiate innate immune responses, this process has never been thoroughly investigated. In this study, we infected larval zebrafish with four different viruses and analyzed whole-fish expression profiles from five groups of fish, including controls, at 10 h after infection. At this early stage of virus infection, 60.28% of the differentially expressed genes displayed the same expression pattern across all viruses, with the majority of immune-related genes downregulated and genes associated with protein synthesis and sterol synthesis upregulated. Furthermore, these protein synthesis- and sterol synthesis-related genes were strongly positively correlated in the expression pattern of the rare key upregulated immune genes, IRF3 and IRF7, which were not positively correlated with any known pattern recognition receptor gene. We hypothesize that viral infection triggered a large amount of protein synthesis that stressed the endoplasmic reticulum and the organism responded to this stress by suppressing the body's immune system while also mediating an increase in steroids. The increase in sterols then participates the activation of IRF3 and IRF7 and triggers the fish's innate immunological response to the virus infection.

Mineral quantitative characterization method based on basis material decomposition model by dual-energy computed tomography.

BACKGROUND: Dual-energy computed tomography (DECT) can reconstruct electron density ρe and effective atomic number Zeff distribution for material discrimination. Image-domain basis material decomposition (IBMD) method is a widely used DECT method. However, IBMD method cannot be used for mineral identification directly due to limitations of complex basis material determination, beam hardening artifacts, and inherent errors caused by approximate empirical formulas. OBJECTIVE: This study proposes an improved IBMD (IIBMD) method to overcome the above limitations. METHODS: In IIBMD method, the composition of basis material is optimized to obtain accurate decomposition coefficients, which enables accurate ρe and Zeff distribution. Moreover, the thickness of basis material is optimized to reduce the effect of beam hardening. Furthermore, two formulas in place of empirical formulas are proposed to calculate ρe and Zeff. Finally, a threshold technique is applied to separate different mineral phases. RESULTS: Numerical simulations and practical experiments using a photon-counting detector CT system are implemented to verify IIBMD method. Results show that the relative errors of ρe and Zeff for seven common minerals are down to 5%, lower than most of the existing DECT methods for rocks. Reasonable volume fraction results of mineral phases are thus obtained through threshold segmentation. CONCLUSIONS: This study demonstrates that the proposed IIBMD method has high practical value in mineralogical identification.

Visual Omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities.

SUMMARY: With the continuous development of high-throughput sequencing technology, bioinformatic analysis of omics data plays an increasingly important role in life science research. Many R packages are widely used for omics analysis, such as DESeq2, clusterProfiler and STRINGdb. And some online tools based on them have been developed to free bench scientists from programming with these R packages. However, the charts generated by these tools are usually in a fixed, non-editable format and often fail to clearly demonstrate the details the researchers intend to express. To address these issues, we have created Visual Omics, an online tool for omics data analysis and scientific chart editing. Visual Omics integrates multiple omics analyses which include differential expression analysis, enrichment analysis, protein domain prediction and protein-protein interaction analysis with extensive graph presentations. It can also independently plot and customize basic charts that are involved in omics analysis, such as various PCA/PCoA plots, bar plots, box plots, heat maps, set intersection diagrams, bubble charts and volcano plots. A distinguishing feature of Visual Omics is that it allows users to perform one-stop omics data analyses without programming, iteratively explore the form and layout of graphs online and fine-tune parameters to generate charts that meet publication requirements. AVAILABILITY AND IMPLEMENTATION: Visual Omics can be used at http://bioinfo.ihb.ac.cn/visomics. Source code can be downloaded at http://bioinfo.ihb.ac.cn/software/visomics/visomics-1.1.tar.gz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Dynamic Transcriptional Landscape of Grass Carp (Ctenopharyngodon idella) Reveals Key Transcriptional Features Involved in Fish Development.

A high-quality baseline transcriptome is a valuable resource for developmental research as well as a useful reference for other studies. We gathered 41 samples representing 11 tissues/organs from 22 important developmental time points within 197 days of fertilization of grass carp eggs in order to systematically examine the role of lncRNAs and alternative splicing in fish development. We created a high-quality grass carp baseline transcriptome with a completeness of up to 93.98 percent by combining strand-specific RNA sequencing and single-molecule real-time RNA sequencing technologies, and we obtained temporal expression profiles of 33,055 genes and 77,582 transcripts during development and tissue differentiation. A family of short interspersed elements was preferentially expressed at the early stage of zygotic activation in grass carp, and its possible regulatory components were discovered through analysis. Additionally, after thoroughly analyzing alternative splicing events, we discovered that retained intron (RI) alternative splicing events change significantly in both zygotic activation and tissue differentiation. During zygotic activation, we also revealed the precise regulatory characteristics of the underlying functional RI events.

Dietary Inclusion of Seabuckthorn (Hippophae rhamnoides) Mitigates Foodborne Enteritis in Zebrafish Through the Gut-Liver Immune Axis.

To help prevent foodborne enteritis in aquaculture, several feed additives, such as herbal medicine, have been added to fish diets. Predictions of effective herb medicines for treating fish foodborne enteritis from key regulated DEGs (differentially expressed genes) in transcriptomic data can aid in the development of feed additives using the Traditional Chinese Medicine Integrated Database. Seabuckthorn has been assessed as a promising candidate for treating grass carp soybean-induced enteritis (SBMIE). In the present study, the SBMIE zebrafish model was used to assess seabuckthorn's therapeutic or preventative effects. The results showed that intestinal and hepatic inflammation was reduced when seabuckthorn was added, either pathologically (improved intestinal villi morphology, less oil-drops) or growth-related (body fat deposition). Moreover, seabuckthorn may block the intestinal p53 signaling pathway, while activating the PPAR signaling pathway and fatty acid metabolism in the liver. 16S rRNA gene sequencing results also indicated a significant increase in OTU numbers and skewed overlapping with the fish meal group following the addition of seabuckthorn. Additionally, there were signs of altered gut microbiota taxa composition, particularly for reduced TM7, Sphingomonas, and Shigella, following the addition of seabuckthorn. Hindgut imaging of fluorescent immune cells in SBMIE larvae revealed the immune regulatory mechanisms at the cellular level. Seabuckthorn may significantly inhibit the inflammatory gathering of neutrophils, macrophages, and mature T cells, as well as cellular protrusions' formation. On the other hand, in larvae, seabuckthorn inhibited the inflammatory aggregation of lck+ T cells but not immature lymphocytes, indicating that it affected intestinal adaptive immunity. Although seabuckthorn did not affect the distribution of intestinal CD4+ cells, the number of hepatic CD4+ cells were reduced in fish from the seabuckthorn supplementation group. Thus, the current data indicate that seabuckthorn may alleviate foodborne gut-liver symptoms by enhancing intestinal mucosal immunity and microbiota while simultaneously inhibiting hepatic adipose disposition, making it a potential additive for preventing fish foodborne gut-liver symptoms.

Whole-genome analysis of Klebsiella pneumoniae from bovine mastitis milk in the U.S.

Dairy cattle mastitis has long been one of the most common and costly diseases in the dairy industry worldwide, due to its significant impact on milk production and animal welfare. Among all mastitis causing bacterial pathogens, Klebsiella pneumoniae causes the largest milk loss. To better understand the genomic features of this population, 180 K. pneumoniae strains isolated from dairy cattle mastitis milk in 11 U.S. states were sequenced. The phylogenetic analysis classified all mastitis-causing K. pneumoniae into two major phylogroups, with exclusive predominance in phylogroup KpI. Analysis of more than 61 sequence types, 51 capsular types and 12 lipopolysaccharide O-antigen types revealed great genomic diversity of this K. pneumoniae population. Approximately 100 gene units in accessory genomes were detected with significantly higher prevalence in bovine mastitis strains, compared to human-sourced or dairy environmental strains. The most notable genes were identified associated with ferric citrate uptake, lactose fermentation and resistance to heavy metals. The acquired antimicrobial resistance genes were identified in sporadic mastitis strains. This comprehensive genomic epidemiological study provides insights for a better understanding of the virulence of mastitis-causing K. pneumoniae strains and may lead to the development of novel diagnostic tools and preventive strategies.

Profiling the Spatial Expression Pattern and ceRNA Network of lncRNA, miRNA, and mRNA Associated with the Development of Intermuscular Bones in Zebrafish.

Intermuscular bones (IBs) are small spicule-like bones in the muscular septum of fish, which affect their edible and economic value. The molecular mechanism of IB development is still uncertain. Numerous studies have shown that the ceRNA network, which is composed of mRNA, lncRNA, and miRNA, plays an important regulatory role in bone development. In this study, we compared the mRNA, lncRNA, and miRNA expression profiles in different IB development segments of zebrafish. The development of IBs includes two main processes, which are formation and growth. A series of genes implicated in the formation and growth of IBs were identified through gene differential expression analysis and expression pattern analysis. Functional enrichment analysis showed that the functions of genes implicated in the regulation of the formation and growth of IBs were quite different. Ribosome and oxidative phosphorylation signaling pathways were significantly enriched during the formation of IBs, suggesting that many proteins are required to form IBs. Several pathways known to be associated with bone development have been shown to play an important role in the growth of IBs, including calcium, ECM-receptor interaction, Wnt, TGF-ß, and hedgehog signaling pathways. According to the targeting relationship and expression correlation of mRNA, lncRNA, and miRNA, the ceRNA networks associated with the growth of IBs were constructed, which comprised 33 mRNAs, 9 lncRNAs, and 7 miRNAs. This study provides new insight into the molecular mechanism of the development of IBs.

De novo screening of disease-resistant genes from the chromosome-level genome of rare minnow using CRISPR-cas9 random mutation.

BACKGROUND: Mutants are important for the discovery of functional genes and creation of germplasm resources. Mutant acquisition depends on the efficiency of mutation technology and screening methods. CRISPR-Cas9 technology is an efficient gene editing technology mainly used for editing a few genes or target sites, which has not been applied for the construction of random mutant libraries and for the de novo discovery of functional genes. RESULTS: In this study, we first sequenced and assembled the chromosome-level genome of wild-type rare minnow (Gobiocypris rarus) as a susceptible model of hemorrhagic disease, obtained a 956.05 Mb genome sequence, assembled the sequence into 25 chromosomes, and annotated 26,861 protein-coding genes. Thereafter, CRISPR-Cas9 technology was applied to randomly mutate the whole genome of rare minnow with the conserved bases (TATAWAW and ATG) of the promoter and coding regions as the target sites. The survival rate of hemorrhagic disease in the rare minnow gradually increased from 0% (the entire wild-type population died after infection) to 38.24% (F3 generation). Finally, 7 susceptible genes were identified via genome comparative analysis and cell-level verification based on the rare minnow genome. CONCLUSIONS: The results provided the genomic resources for wild-type rare minnow, and confirmed that the random mutation system designed using CRISPR-Cas9 technology in this study is simple and efficient and is suitable for the de novo discovery of functional genes and creation of a germplasm resource related to qualitative traits.

Sinomenine Hydrochloride Ameliorates Fish Foodborne Enteritis via α7nAchR-Mediated Anti-Inflammatory Effect Whilst Altering Microbiota Composition.

Foodborne intestinal inflammation is a major health and welfare issue in aquaculture. To prevent enteritis, various additives have been incorporated into the fish diet. Considering anti-inflammatory immune regulation, an effective natural compound could potentially treat or prevent intestinal inflammation. Our previous study has revealed galantamine's effect on soybean induced enteritis (SBMIE) and has highlighted the possible role of the cholinergic anti-inflammatory pathway in the fish gut. To further activate the intestinal cholinergic related anti-inflammatory function, α7nAchR signaling was considered. In this study, sinomenine, a typical agonist of α7nAChR in mammals, was tested to treat fish foodborne enteritis via its potential anti-inflammation effect using the zebrafish foodborne enteritis model. After sinomenine's dietary inclusion, results suggested that there was an alleviation of intestinal inflammation at a pathological level. This outcome was demonstrated through the improved morphology of intestinal villi. At a molecular level, SN suppressed inflammatory cytokines' expression (especially for tnf-α) and upregulated anti-inflammation-related functions (indicated by expression of il-10, il-22, and foxp3a). To systematically understand sinomenine's intestinal effect on SBMIE, transcriptomic analysis was done on the SBMIE adult fish model. DEGs (sinomenine vs soybean meal groups) were enriched in GO terms related to the negative regulation of lymphocyte/leukocyte activation and alpha-beta T cell proliferation, as well as the regulation of lymphocyte migration. The KEGG pathways for glycolysis and insulin signaling indicated metabolic adjustments of α7nAchR mediated anti-inflammatory effect. To demonstrate the immune cells' response, in the SBMIE larva model, inflammatory gatherings of neutrophils, macrophages, and lymphocytes caused by soybean meal could be relieved significantly with the inclusion of sinomenine. This was consistent within the sinomenine group as CD4+ or Foxp3+ lymphocytes were found with a higher proportion at the base of mucosal folds, which may suggest the Treg population. Echoing, the sinomenine group's 16s sequencing result, there were fewer enteritis-related TM7, Sphingomonas and Shigella, but more Cetobacterium, which were related to glucose metabolism. Our findings indicate that sinomenine hydrochloride could be important in the prevention of fish foodborne enteritis at both immune and microbiota levels.

Comprehensive analysis of hub mRNA, lncRNA and miRNA, and associated ceRNA networks implicated in grass carp (Ctenopharyngodon idella) growth traits.

Grass carp (Ctenopharyngodon idella) is the most productive freshwater aquaculture fish in worldwide. However, the molecular mechanism of its growth traits has not been fully elucidated. Whole transcriptome analysis of the brain and hepatopancreas of 29 six-month-old grass carp with different growth rates was performed. Weighted gene co-expression network analysis (WGCNA) was used to construct a weighted gene co-expression network of mRNA, miRNA and lncRNA separately. A total of 35 hub mRNAs, 47 hub lncRNAs and 33 hub miRNAs were identified from the brain, 37 hub mRNAs, 110 hub lncRNAs and 36 hub miRNAs were identified from the hepatopancreas. The ceRNA networks in the brain and hepatopancreas were involved in brain development and nutrient metabolism, respectively. Overall, this is the first investigation of the growth-related transcriptomic characteristics in the brain and hepatopancreas of grass carp, thus will help us to further explore the molecular mechanism of grass carp growth rate.