A Compact Gas-Kinetic Scheme with Scalable Geometric Multigrid Acceleration for Steady-State Computation on 3D Unstructured Meshes

In this paper, we present an advanced high-order compact gas-kinetic scheme (CGKS) for 3D unstructured mixed-element meshes, augmented with a geometric multigrid technique to accelerate steady-state convergence. The scheme evolves cell-averaged flow variables and their gradients on the original mesh. Mesh coarsening employs a two-step parallel agglomeration algorithm using a random hash for cell interface selection and a geometric skewness metric for deletion confirmation, ensuring both efficiency and robustness. For the coarser meshes, first-order kinetic flux vector splitting (KFVS) schemes with explicit or implicit time-stepping are used. The proposed multigrid CGKS is tested across various flow regimes on hybrid unstructured meshes, demonstrating significant improvements. A three-layer V-cycle multigrid strategy, coupled with an explicit forward Euler method on coarser levels, results in a convergence rate up to ten times faster than standard CGKS. In contrast, the implicit lower-upper symmetric Gauss-Seidel (LU-SGS) method offers limited convergence acceleration. Our findings indicate that the explicit multigrid CGKS is highly scalable and effective for large-scale computations, marking a substantial step forward in computational fluid dynamics

In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing

High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies

Migrasome, a migration-dependent organelle

Migrasomes are organelles produced by migrating cells that form on retraction fibers and are released during cell migration. Migrasomes are involved in physiological and pathological processes such as intercellular communication, cell homeostasis maintenance, signal transduction, disease occurrence and development, and cancer metastasis. In addition, methods and techniques for studying migrasomes are constantly evolving. Here, we review the discovery, formation process, regulation, and known functions of migrasomes, summarize the commonly used specific markers of migrasomes, and the methods for observing migrasomes. Meanwhile, this review also discusses the potential applications of migrasomes in physiological processes, disease diagnosis, treatment, and prognosis, and looks forward to their wider application in biomedicine. In addition, the study of migrasomes will also reveal a new perspective on the mechanism of intercellular communication and promote the further development of life science

Regulation Mechanism of MYC Family Transcription Factors in Jasmonic Acid Signalling Pathway on Taxol Biosynthesis

Paclitaxel is an important anticancer drug. The phytohormone jasmonic acid can significantly induce the biosynthesis of paclitaxel in Taxus, but the molecular mechanism has not yet been resolved. To establish the jasmonic acid signalling pathway of Taxus media, based on the gene of the jasmonic acid signalling pathway of Arabidopsis thaliana, sequence analysis was performed to isolate the jasmonic acid signal from the transcriptome, a transcriptional cluster of pathway gene homologs and the full length of 22 genes were obtained by RACE PCR at 5′ and 3′: two EI ubiquitin ligase genes, COI1-1 and COI1-2;7 MYC bHLH type transcription factor (MYC2, MYC3, MYC4, JAM1, JAM2, EGL3, TT8); 12 JAZ genes containing the ZIM domain; and MED25, one of the components of the transcriptional complex. The protein interaction between each were confirmed by yeast two hybridization and bimolecular fluorescence complementation based on similar genes interaction in Arabidopsis. A similar jasmonate signaling pathway was illustrated in T. media. All known paclitaxel biosynthesis genes promoters were isolated by genome walker PCR. To investigate the jasmonate signaling effect on these genes’ expression, the transcription activity of MYC2, MYC3 and MYC4 on these promoters were examined. There are 12, 10 and 11 paclitaxel biosynthesis genes promoters that could be activated by MYC2, MYC3 and MYC4

Bioremediation of Aquaculture Wastewater with Algal-Bacterial Biofilm Combined with the Production of Selenium Rich Biofertilizer

The discharge of aquaculture wastewater and the excessive selenium in aquaculture effluent caused by selenium addition to aquatic feed are posing a serious risk for the marine environment. In this study, batch tests were carried out to investigate the feasibility of utilizing algal–bacterial biofilm for the treatment of selenium-rich aquaculture wastewater. The effects of four different types of commercial biofilm carriers on the attached growth of biofilms and the contaminant removal capacity were examined. The braided cotton biofilm carrier had the best performance on biofilm growth, while in an exponential growth period the dry weight density of the biofilm was above 2.0 g L−1. By utilizing the braided cotton carrier with a hydraulic retention time (HRT) of 6 days, the removal rate of N and P from the raw aquaculture wastewater was 88.5 ± 6.2% and 99.8 ± 0.2%, respectively. After that, the effects of different initial wastewater load ratios (IWLR) and HRT on the effluent quality of the treatment process were studied. The decrease in IWLR and the extension of HRT could improve the treatment performance. The effluent N, P and Se concentrations in the group with 50% IWLR and 6-day HRT were 0.75 ± 0.10 mg L−1, 0.015 ± 0.02 mg L−1, 35.2 ± 3.2 μg L−1, respectively, indicating an effective removal of the main contaminants. The algal–bacterial biofilm harvested from the batch test was rich in N, P and Se, where the Se content was 21.8 ± 3.4 mg kg−1, which has the potential to be used as an Se-rich biofertilizer

The basal transcription factor II H subunit Tfb5 is required for stress response and pathogenicity in the tangerine pathotype ofAlternaria alternata

The basal transcription factor II H (TFIIH) is a multicomponent complex. In the present study, we characterized a TFIIH subunit Tfb5 by analysing loss- and gain-of-function mutants to gain a better understanding of the molecular mechanisms underlying stress resistance and pathogenicity in the citrus fungal pathogen Alternaria alternata. Tfb5 deficiency mutants (ΔAatfb5) decreased sporulation and pigmentation, and were impaired in the maintenance of colony surface hydrophobicity and cell wall integrity. ΔAatfb5 increased sensitivity to ultraviolet light, DNA-damaging agents, and oxidants. The expression of Aatfb5 was up-regulated in the wild type upon infection in citrus leaves, implicating the requirement of Aatfb5 in fungal pathogenesis. Biochemical and virulence assays revealed that ΔAatfb5 was defective in toxin production and cellwall-degrading enzymes, and failed to induce necrotic lesions on detached citrus leaves. Aatfb5 fused with green fluorescent protein (GFP) was localized in the cytoplasm and nucleus and physically interacted with another subunit, Tfb2, based on yeast two-hybrid and co-immunoprecipitation analyses. Transcriptome and Antibiotics & Secondary Metabolite Analysis Shell (antiSMASH) analyses revealed the positive and negative roles of Aatfb5 in the production of various secondary metabolites and in the regulation of many metabolic and biosynthetic processes in A. alternata. Aatfb5 may play a negative role in oxidative phosphorylation and a positive role in peroxisome biosynthesis. Two cutinase-coding genes (AaCut2 and AaCut15) required for full virulence were down-regulated in ΔAatfb5. Overall, this study expands our understanding of how A. alternata uses the basal transcription factor to deal with stress and achieve successful infection in the plant host

Carboxylate, nitrate, sulfonate, and phosphate catalysts for living radical polymerization : via oxygen-iodine halogen bonding catalysis

Four families of oxyanions, i.e., carboxylate, nitrate, phosphate, and sulfonate, were studied as novel catalysts in living (or reversible deactivation) radical polymerization via oxygen-iodine halogen bonding catalysis. Oxyanions with sodium and tetraalkylammonium counter-cations exhibited good catalytic activities and high solubilities in hydrophilic and hydrophobic monomers. These oxyanion catalysts were amenable for methyl methacrylate, functional methacrylates, styrene, and acrylonitrile, and also afforded block copolymers with low dispersities. The catalytic activities of the oxyanions were also theoretically studied using density functional theory (DFT) calculation. The studied four families of oxyanions are abundant in natural and synthetic compounds. Non-Toxic natural carboxylates were successfully used to synthesize well-defined biocompatible polymers. The low cost, low toxicity, and accessibility for a range of polymer designs are attractive features for practical use.NRF (Natl Research Foundation, S’pore)MOE (Min. of Education, S’pore)Accepted versio