Transcription factor EgGRP2A regulates EgFATA expression and promotes oleic acid accumulation in oil palm (Elaeis guineensis).

The oil palm (Elaeis guineensis) is emerging as the world's most important and prolific oilseed crop, celebrated for its impressive oil yield. However, the molecular intricacies that govern lipid metabolism and fatty acid accumulation in oil palm fruits remain relatively underexplored. This study reveals a significant correlation between the expression of EgGRP2A, a transcription factor, and the expression of EgFATA in the oil palm. Yeast one-hybrid analysis and electrophoretic mobility shift assays (EMSA) reveal and confirm the binding interactions between EgGRP2A and the promoter region of EgFATA. Subsequent experiments in oil palm protoplasts show that transient overexpression of EgGRP2A leads to a marked upregulation of EgFATA expression. Conversely, downregulation of EgGRP2A in transgenic oil palm embryoids leads to a significant reduction in EgFATA expression. Metabolite profiling in the transgenic embryoids reveals a significant reduction in unsaturated fatty acids, particularly oleic acid. These findings promise profound insights into the regulatory orchestration of EgFATA and the synthesis of fatty acids, particularly oleic acid, in the oil palm. Furthermore, the results lay the foundation for future breeding and genetic improvement efforts aimed at increasing oleic acid content in oil palm varieties.

DRCNN: decomposing residual convolutional neural networks for time series forecasting.

Recent studies have shown great performance of Transformer-based models in long-term time series forecasting due to their ability in capturing long-term dependencies. However, Transformers have their limitations when training on small datasets because of their lack in necessary inductive bias for time series forecasting, and do not show significant benefits in short-time step forecasting as well as that in long-time step as the continuity of sequence is not focused on. In this paper, efficient designs in Transformers are reviewed and a design of decomposing residual convolution neural networks or DRCNN is proposed. The DRCNN method allows to utilize the continuity between data by decomposing data into residual and trend terms which are processed by a designed convolution block or DR-Block. DR-Block has its strength in extracting features by following the structural design of Transformers. In addition, by imitating the multi-head in Transformers, a Multi-head Sequence method is proposed such that the network is enabled to receive longer inputs and more accurate forecasts are obtained. The state-of-the-art performance of the presented model are demonstrated on several datasets.

Genome-wide DNA Methylation Analysis of Mantle Edge and Mantle Central from Pearl Oyster Pinctada fucata martensii.

DNA methylation is a type of epigenetic modification that alters gene expression without changing the DNA sequence and mediates some cases of phenotypic plasticity. In this study, we identified six DNA methyltransferase (DNMT) genes and two methyl-CpG binding domain protein2 (MBD2) gene from Pinctada fucata martensii. We also analyzed the genome-wide DNA methylation levels of mantle edge (ME) and mantle central (MC) from P. f. martensii via methylated immunoprecipitation sequencing (MeDIP-Seq). Results revealed that both ME and MC had 122 million reads, and had 58,702 and 55,721 peaks, respectively. The obtained methylation patterns of gene elements and repeats showed that the methylation of the protein-coding genes, particularly intron and coding exons (CDSs), was more frequent than that of other genomic elements in the pearl oyster genome. We combined the methylation data with the RNA-seq data of the ME and MC of P. f. martensii and found that promoter, CDS, and intron methylation levels were positively correlated with gene expression levels except the highest gene expression level. We also identified 313 differential methylation genes (DMGs) and annotated 212 of them. These DMGs were significantly enriched in 30 pathways, such as amino acid and protein metabolism, energy metabolism, terpenoid synthesis, and immune-related pathways. This study comprehensively analyzed the methylomes of biomineralization-related tissues and helped enhance our understanding of the regulatory mechanism underlying shell formation.

Evolutionary and functional analysis of MyD88 genes in pearl oyster Pinctada fucata martensii.

Myeloid differentiation factor 88 (MyD88) is an adapter protein that links toll-like receptor and interleukin 1 receptor-mediated signal transduction. In this study, we identified 20 MyD88 genes from eight mollusk genomes and found that MyD88 was expanded in bivalves. This expansion tends to be tandem duplication. Phylogenetic analysis suggested that the tandem duplication of MyD88 was formed before bivalve differentiation. All of the identified MyD88 contained both of death domain (DD) and toll/interleukin-1 receptor (TIR) domain, and 13 mollusks MyD88 have low complexity regions (LCRs), which were not found in the MyD88 from humans and zebrafish. The genomic structure showed that most of the mollusk MyD88 (14 of 19) contained five conserved introns, four of which were found in humans and zebrafish. Furthermore, the cDNA full length of PfmMyD88-2 (one of the two identified MyD88 in Pincatada fucata martensii) was obtained with 1591 bp, including 260 bp of 5'UTR, 257 bp of 3'UTR, and 1077 bp of open reading frame encoding 358 amino acids. Quantitative real-time PCR analysis demonstrated that PfmMyD88-2 mRNA was widely expressed in all detected tissues. The highest expression level was in the gills and followed by hepatopancreas and feet. After lipopolysaccharide stimulation, PfmMyD88-2 expression level increased and reached the highest level at 12 h and then gradually declined to the normal level. Over-expression of PfmMyD88-2 in HEK293T increased the luciferase activity of the pNF-κB-Luc reporter. We also identified that PfmmiR-4047 could regulate the expression of PfmMyD88-2. These results help us elucidate the mechanism underlying mollusk immune response.

Study on Morphology and Rheological Property of Organoclay Dispersions in Soybean Oil Fatty Acid Ethyl Ester over a Wide Temperature Range.

This work attempted to establish the relationship between the dispersion morphology and the viscous flow behavior of clay dispersions in soybean oil fatty acid ethyl ester (FAEE) at 2 and 65 °C. The clays used in this study include raw montmorillonite (Mt) and three kinds of organoclays prepared by ion exchange modification of Mt by cetyltrimethylammonium chloride (OC16), dihexadecyldimethylammonium chloride (ODC16), and trihexadecylmethylammonium chloride (OTC16), respectively. The X-ray diffraction and water contact angle results demonstrated that greater alkyl chain number of surfactants led to greater interlayer space and stronger hydrophobicity of organoclays. Due to the good affinity of the surfactant and FAEE, OC16 exhibited the most stable dispersion in FAEE between 2-65 °C, which resulted in the best flat rheological property. The molecular structures of multiple chain surfactants were quite different from that of FAEE, resulting in weak affinity between organoclays (ODC16 and OTC16) and FAEE. The sheets of ODC16 and OTC16 tended to aggregate at 2 °C, forming a gel structure, thus significantly increasing the low shear rate viscosity (LSRV) and yield stress. At 65 °C, with the expansion of FAEE and the stronger thermal motion of sheets, the dispersions of ODC16 and OTC16 were improved, destroying the original gel structure and resulting in significant decreases in LSRV and yield stress. This study confirmed that stable clay/FAEE dispersions tended to exhibit flat rheology, which could serve as a basis for the application of clay/biodiesel dispersion in deep-water drilling.

Transcriptome analysis of growth heterosis in pearl oyster Pinctada fucata martensii.

Heterosis improves growth and survival of shellfish species. Although breeders have widely exploited heterosis, its underlying molecular mechanisms remain unclear. In this study, a 2 × 2 complete diallel cross was facilitated between two full-sib families to produce two inbred families (A and D) and their reciprocal hybrid families (B and C) of pearl oyster Pinctada fucata martensii. Growth traits of the four families were compared at the adult stages. Transcriptome analysis was conducted on the four families using an Illumina sequencing platform. The results revealed that the growth traits of the four families significantly varied (P < 0.05). The mid-parent heterosis values of shell length, shell height, shell width, shell weight, and total weight were 12.9%, 14.9%, 18.2%, 17.2%, and 33.2%, respectively. The B- and C-inbred (A and D) triads had 79 and 68 differentially expressed genes (DEGs), respectively, which were dominantly nonadditive, including overdominance, underdominance, and low-parent dominance. Gene ontology term analysis showed that the DEGs in the B- and C-inbred triads were enriched for metabolic process, cellular process cell part, binding, and catalytic activity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that the DEGs in the B- and C-inbred triads were involved in focal adhesion, the P13K-Akt signaling pathway, the mRNA surveillance pathway, and the focal adhesion pathway. The reliability of the sequencing data was confirmed by real-time polymerase chain reaction analysis of six growth-related genes. The findings of this study provide new insights into heterosis for growth traits and the design of genetic breeding programs for this species.

Nanoscale Laponite as a Potential Shale Inhibitor in Water-Based Drilling Fluid for Stabilization of Wellbore Stability and Mechanism Study.

Shale hydration is the main reason causing wellbore instability in oil and gas drilling operations. In this study, nanoscale laponite as a shale inhibitor was employed to stabilize wellbores. The inhibition property of laponite suspensions was evaluated by an immersion experiment, linear swelling measurement, and a shale recovery test. Then the shale inhibition mechanism was studied by using capillary suction time (CST) measurement, a thixotropy study, plugging performance evaluation, and related theoretical analysis. Evaluation experiment results showed that laponite had a better inhibition property than widely used inhibitors of potassium chloride (KCl) and poly(ester amine) (PA). The mechanism study revealed that integration of several factors strengthened the inhibition property of laponite suspensions. Laponite nanoparticles could plug interlayer spaces of clays by electrostatic interaction to reduce water invasion; the "house of cards" structure of laponite suspensions enables large CST values and low free water contents; the excellent thixotropy of a laponite nanofluid could allow a nanofilm to form in order to reduce water invasion into the formation; the nanoscale laponite particles could substantially reduce the shale permeability and form less porous surfaces. Furthermore, laponite could considerably decrease the filtrate volume of the drilling fluid, while KCl and PA had negative influences on the properties of the drilling fluid. This approach described herein might provide an avenue to inhibit shale hydration.

Molecular characterization of the BMP7 gene and its potential role in shell formation in Pinctada martensii.

Bone morphogenetic protein 7 (BMP7), also called osteogenetic protein-1, can induce bone formation. In this study, the obtained full-length cDNA of BMP7 from Pinctada martensii (Pm-BMP7) was 2972 bp, including a 5'-untranslated region (UTR) of 294 bp, an open reading fragment of 1290 bp encoding a 429 amino acid polypeptide and a 3'-UTR of 1388 bp. The deduced protein sequence of Pm-BMP7 contained a signal peptide, a pro-domain and a mature peptide. The mature peptide consisted of 135 amino acids and included a transforming growth factor ß family domain with six shared cysteine residues. The protein sequence of Pm-BMP7 showed 66% identity with that from Crassostrea gigas. Two unigenes encoding Pm-BMPRI (Pm-BMP receptor I) and Pm-BMPRII were obtained from the transcriptome database of P. martensii. Tissue expression analysis demonstrated Pm-BMP7 and Pm-BMPRI were highly expressed in the mantle (shell formation related-tissue), while Pm-BMPRII was highly expressed in the foot. After inhibiting Pm-BMP7 expression using RNA interference (RNAi) technology, Pm-BMP7 mRNA was significantly down-regulated (p < 0.05) in the mantle pallium (nacre formation related-tissue) and the mantle edge (prismatic layer formation related-tissue). The microstructure, observed using a scanning electron microscope, indicated a disordered growth status in the nacre and obvious holes in the prismatic layer in the dsRNA-Pm-BMP7 injected-group. These results suggest that Pm-BMP7 plays a crucial role in the nacre and prismatic layer formation process of the shell.