Correlation between DNA methylation and transcriptomic changes in golden Asian sea bass (Lates calcarifer): An integrated approach.

BackgroundDNA cytosine methylation is an important epigenetic modification that has significant effects on a variety of biological processes in animals. Avian species hold a crucial position in evolutionary history. In this study, we used whole-genome bisulfite sequencing (MethylC-seq) to generate single base methylation profiles of lungs in two genetically distinct and highly inbred chicken lines (Fayoumi and Leghorn) that differ in genetic resistance to multiple pathogens, and we explored the potential regulatory role of DNA methylation associated with immune response differences between the two chicken lines.MethodsThe MethylC-seq was used to generate single base DNA methylation profiles of Fayoumi and Leghorn birds. In addition, transcriptome profiling using RNA–seq from the same chickens and tissues were obtained to interrogate how DNA methylation regulates gene transcription on a genome-wide scale.ResultsThe general DNA methylation pattern across different regions of genes was conserved compared to other species except for hyper-methylation of repeat elements, which was not observed in chicken. The methylation level of miRNA and pseudogene promoters was high, which indicates that silencing of these genes may be partially due to promoter hyper-methylation. Interestingly, the promoter regions of more recently evolved genes tended to be more highly methylated, whereas the gene body regions of evolutionarily conserved genes were more highly methylated than those of more recently evolved genes. Immune-related GO (Gene Ontology) terms were significantly enriched from genes within the differentially methylated regions (DMR) between Fayoumi and Leghorn, which implicates DNA methylation as one of the regulatory mechanisms modulating immune response differences between these lines.ConclusionsThis study establishes a single-base resolution DNA methylation profile of chicken lung and suggests a regulatory role of DNA methylation in controlling gene expression and maintaining genome transcription stability. Furthermore, profiling the DNA methylomes of two genetic lines that differ in disease resistance provides a unique opportunity to investigate the potential role of DNA methylation in host disease resistance. Our study provides a foundation for future studies on epigenetic modulation of host immune response to pathogens in chickens.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2098-8) contains supplementary material, which is available to authorized users.

BackgroundDNA methylation is a crucial epigenetic mechanism that regulates gene expression during plant growth and development. However, the role of DNA methylation in regulating the organ-specific functions of the invasive weed Mikania micrantha remains unknown.ResultsHere, we generated DNA methylation profiles for M. micrantha and a local congeneric species, Mikania cordata, in three vegetative organs (root, stem, and leaf) using whole-genome bisulfite sequencing. The results showed both differences and conservation in methylation levels and patterns between the two species. Combined with transcriptome data, we found that DNA methylation generally inhibited gene expression, with varying effects depending on the genomic region and sequence context (CG, CHG, and CHH). Genes overlapping with differentially methylated regions (DMRs) were more likely to be differentially expressed between organs, and DMR-associated upregulated differentially expressed genes (DEGs) were enriched in organ-specific pathways. A comparison between photosynthetic (leaf) and non-photosynthetic (root) organs of M. micrantha further confirmed the regulatory role of DNA methylation in leaf-specific photosynthesis. Integrating small RNA-Seq data revealed that 24-nt small interfering RNAs (siRNAs) were associated with CHH methylation in gene-rich regions and regulated CHH methylation in the flanking regions of photosynthesis-related genes.ConclusionThis study provides insights into the complex regulatory role of DNA methylation and siRNAs in organ-specific functions and offers valuable information for exploring the invasive characteristics of M. micrantha from an epigenetic perspective.

Aims: Vibrio harveyi causes vibriosis to Asian seabass ( Lates calcarifer ). The disease spreads rapidly among fish stocked in the same cage. It causes high mortality especially in weak and small sized fish stocked at high density in poorly managed net cage. Study to determine the virulence levels of the bacterial pathogen in various aquaculture animals is a key to prevent vibriosis in marine aquaculture. Methodology and Result: Isolation of bacteria from diseased Asian seabass was done using tryptic soy agar (TSA) and thiosulphate citrate bile sucrose agar (TCBS) plates. Virulence of two strains of Vibrio harveyi (VHJR4 and VHJR7) was tested against clinically healthy aquaculture animals. The analysis revealed that the two bacterial strains differ in pathogenicity. The V. harveyi strain VHJR7 was virulent to Asian seabass at 1.40 x 10 4 c.f.u. g �1 , humpback grouper (Cromileptis altivelis ) at LD 50 8.33 x 10 3 c.f.u. g �1 and black tiger shrimp ( Penaeus monodon ) at LD 50 3.26 x 10 4 c.f.u. g �1 , respectively. The V. harveyi strain VHJR4 was not virulent to Asian seabass and humpback grouper but it caused mortality to black tiger shrimp at LD 50 1.32 x 10 6 c.f.u. g �1 . Phenotypically, the two strains shared most of the biochemical features except that the V. harveyi strain VHJR7 was a urease positive and grew at 8.5 % NaCl, and at 10 °C. The percentage similarity of nucleotide sequences of 16S rDNA in V. harveyi VHJR4 and V. harveyi VHJR7 was higher (99 %) but reduced at 95 % in hemolysin gene. Conclusion, significance and impact of study: Pathogenic strain of V. harveyi causes mortality and affects aquaculture production of Asian seabass. Hence, vaccine development against the bacterial pathogen is urgently needed for sustainability of Asian seabass aquaculture in Malaysia.

Acute changes in DNA methylation in relation to 24 h personal air pollution exposure measurements: A panel study in four European countries

Vibriosis is a bacterial disease caused by Vibrio harveyi (V. harveyi; Vh ) that poses a substantial threat to Asian seabass (Lates calcarifer) aquaculture. In this study, we investigated alternative approaches to conventional injection vaccination for prevention of V. harveyi in Asian seabass. The first approach involved an immersion prime with heat-inactivated V. harveyi vaccine, followed by two oral booster doses (day 14-18 and day 28-32). Immunized fish demonstrated higher expression levels of immune genes (i.e. TNFα, IL1β, CD4, CD8, and IgM) following the immersion prime and the first oral booster dose, peaking at 14 and 28 days post vaccination (dpv). Specific antibodies (IgM) were detected in both systemic and mucosal compartments as early as 7 dpv and exhibited steady increases, reaching their peaks at 21 and 35 dpv. A laboratory challenge test at day 49 dpv showed relatively high protection, with a relative percent survival (RPS) of 72.22% ± 7.86%. The promising immersion prime-oral booster vaccination strategy warranted further improvement. In the second approach, we explored whether the integration of oxygen nanobubbles-enriched water (ONB) and positively charged chitosan (CS) can enhance antigen uptake to fish gills during immersion priming and improve immunological responses post oral booster. We compared antigen uptake in fish gills, antibody response and vaccine efficacy for four different combinations of vaccine with ONB and CS, and two control groups. Pre-exposure to ONB and CS prior to vaccine application resulted in superior antigen uptake and anti-V. harveyi antibody (IgM) production in both serum and mucus compared to other formulas. We further evaluated the integration of an oral booster (4.22 × 108 CFU/g, at day 21-25) in a vaccine trial experiment to improve the survival rates post exposure to V. harveyi. Antibody responses were measured weekly for over 42 days. Vaccine efficacy was assessed through an intraperitoneal challenge injection with 1.82 × 105 CFU/fish of virulent V. harveyi. The expression of immune-related genes (IL1β, TNFα, CD4, CD8, IgT) and antibody levels were assessed at 1, 3, and 7 day (s) post challenge (dpc). The results revealed that antibody level the group pre-exposed to ONB and CS were consistently higher than other groups post immersion immunization and oral booster. After challenge with V. harveyi, fish in this group exhibited the highest expression levels of immune-related genes in the gills, head kidney, and spleen on 1, 3, and 7 dpc compared to the other groups. Lastly, the group exposed to complex of ONB-CS and vaccine had a higher RPS (p < 0.05) of 63% ± 10.5% compared with the controls at 40.7% ± 10.5% and 25.9% ± 10.5%, respectively. In conclusion, pre-mixing of CS with ONB, followed by V. harveyi vaccine to form the ONB-CS-Vac complex, represents a promising immersion vaccination strategy. This novel approach can enhance antigen uptake, stimulate immunological responses, and improve survival of Asian seabass against vibriosis.

The Asian seabass (Lates calcarifer) is an important marine food fish in Southeast Asia. To facilitate a selective breeding program conducted in Indonesia, we genotyped 29 Asian seabass specimens collected from four wild populations in the Wallacea Region originating from coastal waters in two seaways: the Makassar Strait (Bulungan in North Kalimantan and Maros in South Sulawesi) and the Gulf of Bone (Siwa and Bone in South Sulawesi). We used four polymorphic markers with a random amplified polymorphic DNA (RAPD) method. A total of 43 alleles were detected at four loci across the four populations, four of which were shared by all the accessions while 39 were polymorphic. Of these 43 alleles, 34.88% were unique, with 46.67% in the Gulf of Bone and 53.33% in the Makassar Strait. Asian seabass within-population genetic distance was greater in Bone Bay than the Makassar Strait, and an ongoing speciation phenomenon is suspected. The greatest genetic distance (0.291) was between the Asian seabass populations from Bulungan, North Kalimantan and Cenranae River estuary, Bone Regency; the lowest (0.086) was between the Bulungan and Maros populations. In the phylogenetic analysis, Gulf of Bone and Makassar Strait specimens formed separate clades. Commercial scale cross-breeding between Asian seabass from Makassar Strait and the Gulf of Bone may produce highly adaptable seed. These results will be helpful in future Asian seabass breeding programs as well as for optimising management and conservation strategies for wild Asian seabass populations.

In vitro lead exposure changes DNA methylation and expression of IGF2 and PEG1/MEST

PurposeUveal melanoma (UM) is an aggressive malignancy, in which nearly 50% of the patients die from metastatic disease. Aberrant DNA methylation is recognized as an important epigenomic event in carcinogenesis. Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable source of tumor tissue, and recent technology has enabled the use of these samples in genome-wide DNA methylation analyses. Our aim was to investigate differential DNA methylation in relation to histopathological classification and survival data. In addition we sought to identify aberrant DNA methylation of genes that could be associated with metastatic disease and poor survival. MethodsFFPE samples from UM patients (n = 23) who underwent enucleation of the eye in the period 1976–1989 were included. DNA methylation was assessed using the Illumina Infinium HumanMethylation450 array and coupled to histopathological data, Cancer Registry of Norway- (registered UM metastasis) and Norwegian Cause of Death Registry- (time and cause of death) data. Differential DNA methylation patterns contrasting histological classification, survival data and clustering properties were investigated. Survival groups were defined as “Early metastasis” (metastases and death within 2–5 years after enucleation, n = 8), “Late metastasis” (metastases and death within 9–21 years after enucleation, n = 7) and “No metastasis” (no detected metastases ≥18 years after enucleation, n = 8). A subset of samples were selected based on preliminary multi-dimensional scaling (MDS) plots, histopathological classification, chromosome 3 status, survival status and clustering properties; “Subset Early metastasis” (n = 4) vs “Subset No metastasis” (n = 4). Bioinformatics analyses were conducted in the R statistical software. Differentially methylated positions (DMPs) and differentially methylated regions (DMRs) in various comparisons were assessed. Gene expression of relevant subgroups was determined by microarray analysis and quantitative reverse-transcription polymerase chain reaction (qRT-PCR). ResultsDNA methylation analyses identified 2 clusters that separated the samples according to chromosome 3 status. Cluster 1 consisted of samples (n = 5) with chromosome 3 disomy (D3), while Cluster 2 was comprised of samples (n = 15) with chromosome 3 monosomy (M3). 1212 DMRs and 9386 DMPs were identified in M3 vs D3. No clear clusters were formed based on our predefined survival groups (“Early”, “Late”, “No”) nor histopathological classification (Epithelioid, Mixed, Spindle). We identified significant changes in DNA methylation (beta FC ≥ 0.2, adjusted p < 0.05) between two sample subsets (n = 8). “Subset Early metastasis” (n = 4) vs “Subset No metastasis” (n = 4) identified 348 DMPs and 36 DMRs, and their differential gene expression by microarray showed that 14 DMPs and 2 DMRs corresponded to changes in gene expression (FC ≥ 1.5, p < 0.05). RNF13, ZNF217 and HYAL1 were hypermethylated and downregulated in “Subset Early metastasis” vs “Subset No metastasis” and could be potential tumor suppressors. TMEM200C, RGS10, ADAM12 and PAM were hypomethylated and upregulated in “Subset Early metastasis vs “Subset No metastasis” and could be potential oncogenes and thus markers of early metastasis and poor prognosis in UM. ConclusionsDNA methylation profiling showed differential clustering of samples according to chromosome 3 status: Cluster 1 (D3) and Cluster 2 (M3). Integrated differential DNA methylation and gene expression of two subsets of samples identified genes associated with early metastasis and poor prognosis. RNF13, ZNF217 and HYAL1 are hypermethylated and candidate tumor suppressors, while TMEM200C, RGS10, ADAM12 and PAM are hypomethylated and candidate oncogenes linked to early metastasis. UM FFPE samples represent a valuable source for methylome studies and enable long-time follow-up.

Asian sea bass (Lates calcarifer Bloch, 1790) is a euryhaline fish widely cultured in Asia and Australia. Although it is common to culture Asian sea bass at different salinities, osmoregulatory responses of Asian sea bass during acclimation to various salinities have not been fully observed. In this study, we used scanning electron microscopyto observe the morphology of the ionocyte apical membrane of Asian sea bass acclimated to fresh water (FW), 10‰ brackish water (BW10), 20‰ brackish water (BW20), and seawater (SW; 35‰). Three types of ionocytes were identified in FW and BW fish: (I) flat type with microvilli, (II) basin type with microvilli, and (III) small- hole type. Flat type I ionocytes were also observed in the lamellae of the FW fish. In contrast, two types of ionocytes were identified in SW fish: (III) small-hole type and (IV) big-hole type. Furthermore, we observed Na+ , K+ -ATPase (NKA) immunoreactive cells in the gills, which represent the localization of ionocytes. The highest protein abundance was observed in the SW and FW groups, whereas the highest activity was observed in the SW group. In contrast, the BW10 group had the lowest protein abundance and activity. This study demonstrates the effects of osmoregulatory responses on the morphology and density of ionocytes, as well as protein abundance and activity of NKA. In this study, we found that Asian sea bass had the lowest osmoregulatory response in BW10, because the lowest amounts of ionocytes and NKA were required to maintain osmolality at this salinity.

This study investigated gonadal stages in Asian sea bass ( Lates calcarifer ) using portable ultrasonography (Sonosite Edge II, 6–13 MHz), with histological validation of female (primary oocyte, early vitellogenic, ripe) and male (ripe) stages. Distinct echogenicity patterns differentiated sexes, and ultrasound‐based gonad measurements showed strong correlations with actual dimensions (ovary length R 2 = 0.9942, ovary width R 2 = 0.9886, testis length R 2 = 0.9857, testis width R 2 = 0.9793). Deep learning models achieved 99.9% accuracy for sexual maturity prediction (DenseNet‐161) and 99.8% for sex classification (VGG16). CNN regression with L1 and L2 regularization was used to predict oocyte diameters. The MAE (mean absolute error) was 6.31 µm for minimum and 5.20 µm for maximum oocyte diameter, which is less than 1.82% of the actual oocyte diameter (256–544 µm). These results, along with averaging over 10‐fold and small confidence intervals, indicate the robustness of the classification and regression methods. This raises the possibility of automating the classification of the fish reproductive stage by combining deep learning with ultrasound technologies and further developing contactless underwater ultrasonographic assessment of gonadal maturation in commercially important fin fish species. It also reduces the dependency on experts to infer sexual maturation details from ultrasound scans. The developed machine learning model is deployed in real‐time processor, Nvidia Orin, through which real‐time testing is carried out and the results are validated.

Development of aeration devices and feeding frequencies for oxygen concentration improvement in 60-tones freshwater recirculating aquaculture and biofloc ponds of Asian seabass (Lates calcarifer) rearing

Lc-ms-based lipidomics analyses revealed changes in lipid profiles in Asian sea bass (Lates calcarifer) with dielectric barrier discharge (DBD) atmospheric plasma treatment

Low Levels of Global (LINE) and CDH13 Methylation at Diagnosis and Rapid Clearance of Marrow Blasts Correlate with A Better Haematological Response to Azacitidine in Patients with Newly Diagnosed and Refractory/Relapsed AML Not Eligible for or Resistant to Chemotherapy: A Multi-Centre Phase I/II-Study of the East German Haematology and Oncology Study Group (OSHO).

Aldehyde Dehydrogenase Activity in the Leukemic Stem Cell Compartment Uncovers Opposing Methylation Patterns of Leukemia Stem Cells in AML

Birth weight is a complex multifactorial trait relevant to health states and disease risks in later life. The placenta is essential for proper fetal growth and facilitates gas, nutrient, and waste exchange between the mother and developing fetus. How changes in placental DNA methylation affect fetal birth weight remains to be fully elucidated. In this study, we used whole-genome bisulfite sequencing and RNA sequencing to reveal a global map of DNA methylation and gene expression changes between the placentas of highest birth weight and lowest birth weight piglets in the same litters. The transcriptome analysis identified 1682 differential expressed genes and revealed key transcriptional properties in distinct placentas. We also identified key transcription factors that may drive the differences in DNA methylome patterns between placentas. The decrease in DNA methylation level in the promoter was associated with the transcriptional activation of genes associated with angiogenesis, extracellular matrix remodeling, and transmembrane transport. Our results revealed the regulatory role of DNA methylation in gene transcription activity leading to the differences in placental morphological structures and birth weights of piglets. These results could provide novel clues to clarify the underlying regulatory mechanisms of placental development and fetal growth.