MULTI-SCALE MODELING AND COMPUTATIONS

In the rarefied gas dynamics, the classic kinetic models are more accurate and complicated, while the fluid models are much simpler but fail in some cases. In this thesis, we propose a new local up-scaling model to couple Euler equations with the kinetic model when the previous up-scaling model in [19] does not apply, e.g. when the Boltzmann equation is solved by the particle method, like DSMC. By means of the first order Chapman-Enskog expansion we propose a new NSLU model to couple the Navier-Stokes equations with the kinetic models. We also propose the zero-moment projection based on the macro-micro decomposition ([34]) to correct the non-fluid part in the up-scaling models. Numerical tests of these local up-scaling models have been done in various multi-scale problems, including the Jin-Xin relaxation model for the traveling shock, 1D1D BGK model for the dynamics of a small perturbation of an equilibrium, 1D3D BGK model for the stationary shock and the simulation of a planar Couette flow by direct simulation of Monte Carlo (DSMC) for the Boltzmann equation. The implicit-explicit scheme for the relaxation models is applied, which is shown to preserve the positiveness of the distribution function, the conservation laws and entropy inequality. Numerical results show that the zero-projection is necessary to ensure the stability and accuracy for the up-scaling models, especially when non-kinetic schemes are applied in the moment equations. NSLU model must be applied to replace the up-scaling model in [19] if the macroscopic approximation is the viscous fluid. The similar scaling exists in the relaxation-time model for the semiconductor device when electric field is low. The DrDiLU model based on drift-diffusion model for the diode is proposed which is similar to NSLU model for the rarefied gas. Numerical experiments show it is stable and accurate compared with the results from the relaxation-time model

Metabolomic and transcriptomic responses of Adiantum (Adiantum nelumboides) leaves under drought, half-waterlogging, and rewater conditions

Introduction:Adiantum nelumboides (Adiantum) is an endangered fern with a narrow distribution along the Yangtze River in China. Due to its cliff-dwelling habit, it experiences water stress conditions, which further endangers its survival. However, no information is available about its molecular responses to drought and half-waterlogging conditions.Methods: Here, we applied five and ten days of half-waterlogging stress, five days of drought stress, and rewatering after five days of drought stress, and studied the resulting metabolome profiles and transcriptome signatures of Adiantum leaves.Results and Discussion: The metabolome profiling detected 864 metabolites. The drought and half-waterlogging stress induced up-accumulation of primary and secondary metabolites including amino acids and derivatives, nucleotides and derivatives, flavonoids, alkaloids, and phenolic acid accumulation in Adiantum leaves. Whereas, rewatering the drought-stressed seedlings reversed most of these metabolic changes. Transcriptome sequencing confirmed the differential metabolite profiles, where the genes enriched in pathways associated with these metabolites showed similar expression patterns. Overall, the half-waterlogging stress for 10 days induced large-scale metabolic and transcriptomic changes compared to half-waterlogging stress for 05 days, drought stress for 05 days or rewatering for 05 days.Conclusion: This pioneering attempt provides a detailed understanding of molecular responses of Adiantum leaves to drought and half-waterlogging stresses and rewater conditions. This study also provides useful clues for the genetic improvement of Adiantum for drought/half-waterlogging stress tolerance

Moderate Dietary Protein Restriction Optimized Gut Microbiota and Mucosal Barrier in Growing Pig Model

Appropriate protein concentration is essential for animal at certain stage. This study evaluated the effects of different percentages of dietary protein restriction on intestinal health of growing pigs. Eighteen barrows were randomly assigned to a normal (18%), low (15%), and extremely low (12%) dietary protein concentration group for 30 days. Intestinal morphology and permeability, bacterial communities, expressions, and distributions of intestinal tight junction proteins, expressions of biomarkers of intestinal stem cells (ISCs) and chymous bacterial metabolites in ileum and colon were detected. The richness and diversity of bacterial community analysis with Chao and Shannon index were highest in the ileum of the 15% crude protein (CP) group. Ileal abundances of Streptococcaceae and Enterobacteriaceae decreased respectively, while beneficial Lactobacillaceae, Clostridiaceae_1, Actinomycetaceae, and Micrococcaceae increased their proportions with a protein reduction of 3 percentage points. Colonic abundances of Ruminococcaceae, Christensenellaceae, Clostridiaceae_1, Spirochaetaceae, and Bacterodales_S24-7_group declined respectively, while proportions of Lachnospiraceae, Prevotellaceae, and Veillonellaceae increased with dietary protein reduction. Concentrations of most bacterial metabolites decreased with decreasing dietary protein concentration. Ileal barrier function reflected by expressions of tight junction proteins (occludin, zo-3, claudin-3, and claudin-7) did not show significant decrease in the 15% CP group while sharply reduced in the 12% CP group compared to that in the 18% CP group. And in the 15% CP group, ileal distribution of claudin-3 mainly located in the cell membrane with complete morphological structure. In low-protein treatments, developments of intestinal villi and crypts were insufficient. The intestinal permeability reflected by serous lipopolysaccharide (LPS) kept stable in the 15% CP group while increased significantly in the 12% CP group. The expression of ISCs marked by Lgr5 slightly increased in ileum of the 15% CP group. Colonic expressions of tight junction proteins declined in extremely low protein levels. In conclusion, moderate protein restriction (15% CP) can optimize the ileal microbiota structure via strengthening beneficial microbial populations and suppressing harmful bacterial growth and altering the function of ileal tight junction proteins as well as epithelial cell proliferation

The toxicity of selenium and mercury in Suaeda salsa after 7-days exposure

Mercury is one of the major pollutants in the ocean, selenium causes toxicity beyond a certain limit, but there are few comparative toxic studies between them in halophytes. The study was to investigate the toxic effects of selenium (Se4+) and mercury (Hg2+) in halophyte Suaeda salsa at the level of genes, proteins and metabolites after exposure for 7 days. By integrating the results of proteomics and metabolomics, the pathway changed under different treatments were revealed. In Se4+-treated group, the changed 3 proteins and 10 metabolites participated in the process of substance metabolism (amino acid, pyrimidine), citrate cycle, pentose phosphate pathway, photosynthesis, energy, and protein biosynthesis. In Hg2+-treated group, the changed 10 proteins and 10 metabolites were related to photosynthesis, glycolysis, substance metabolism (cysteine and methionine, amino acid, pyrimidine), ATP synthesis and binding, tolerance, sugar-phosphatase activity, and citrate cycle. In Se4++ Hg2+-treated group, the changed 5 proteins an 12 metabolites involved in stress defence, iron ion binding, mitochondrial respiratory chain, structural constituent of ribosome, citrate cycle, and amino acid metabolism. Furthermore, the separate and combined selenium and mercury both inhibited growth of S. salsa, enhanced activity of antioxidant enzymes (superoxide dismutase, peroxidase and catalase), and disturbed osmotic regulation through the genes of choline monoxygenase and betaine aldehyde dehydrogenase. Our experiments also showed selenium could induce synergistic effects in S. salsa. In all, we successfully characterized the effects of selenium and mercury in plant which was helpful to evaluate the toxicity and interaction of marine pollutants

Two goose-type lysozymes in Mytilus galloprovincialis: possible function diversification and adaptive evolution.

Two goose-type lysozymes (designated as MGgLYZ1 and MGgLYZ2) were identified from the mussel Mytilus galloprovincialis. MGgLYZ1 mRNA was widely expressed in the examined tissues and responded sensitively to bacterial challenge in hemocytes, while MGgLYZ2 mRNA was predominately expressed and performed its functions in hepatopancreas. However, immunolocalization analysis showed that both these lysozymes were expressed in all examined tissues with the exception of adductor muscle. Recombinant MGgLYZ1 and MGgLYZ2 could inhibit the growth of several Gram-positive and Gram-negative bacteria, and they both showed the highest activity against Pseudomonas putida with the minimum inhibitory concentration (MIC) of 0.95-1.91 µM and 1.20-2.40 µM, respectively. Protein sequences analysis revealed that MGgLYZ2 had lower isoelectric point and less protease cutting sites than MGgLYZ1. Recombinant MGgLYZ2 exhibited relative high activity at acidic pH of 4-5, while MGgLYZ1 have an optimum pH of 6. These results indicated MGgLYZ2 adapted to acidic environment and perhaps play an important role in digestion. Genomic structure analysis suggested that both MGgLYZ1 and MGgLYZ2 genes are composed of six exons with same length and five introns, indicating these genes were conserved and might originate from gene duplication during the evolution. Selection pressure analysis showed that MGgLYZ1 was under nearly neutral selection while MGgLYZ2 evolved under positive selection pressure with three positively selected amino acid residues (Y(102), L(200) and S(202)) detected in the mature peptide. All these findings suggested MGgLYZ2 perhaps served as a digestive lysozyme under positive selection pressure during the evolution while MGgLYZ1 was mainly involved in innate immune responses

A novel C-type lysozyme from Mytilus galloprovincialis: insight into innate immunity and molecular evolution of invertebrate C-type lysozymes.

A c-type lysozyme (named as MgCLYZ) gene was cloned from the mussel Mytilus galloprovincialis. Blast analysis indicated that MgCLYZ was a salivary c-type lysozyme which was mainly found in insects. The nucleotide sequence of MgCLYZ was predicted to encode a polypeptide of 154 amino acid residues with the signal peptide comprising the first 24 residues. The deduced mature peptide of MgCLYZ was of a calculated molecular weight of 14.4 kD and a theoretical isoelectric point (pI) of 8.08. Evolution analysis suggested that bivalve branch of the invertebrate c-type lysozymes phylogeny tree underwent positive selection during evolution. By quantitative real-time RT-PCR (qRT-PCR) analysis, MgCLYZ transcript was widely detected in all examined tissues and responded sensitively to bacterial challenge in hemocytes and hepatopancreas. The optimal temperature and pH of recombinant MgCLYZ (rMgCLYZ) were 20°C and 4, respectively. The rMgCLYZ displayed lytic activities against Gram-positive bacteria including Micrococcus luteus and Staphyloccocus aureus, and Gram-negative bacteria including Vibrio anguillarum, Enterobacter cloacae, Pseudomonas putida, Proteus mirabilis and Bacillus aquimaris. These results suggest that MgCLYZ perhaps play an important role in innate immunity of M. galloprovincialis, and invertebrate c-type lysozymes might be under positive selection in a species-specific manner during evolution for undergoing adaptation to different environment and diverse pathogens

Risk Assessment of Heavy Metals Pollution in Fishing Ports Using an Integrated Biomarker Response Approach

Fishing ports play an essential role in fisheries development and supply chains, as all catches are landed through fishing ports to enter the seafood market. Frequent and intensive fishing activities inevitably affect the fishing port ecosystem by discharging sewage and waste oil from sources such as fishing vessels, leaching ship paint, and operating wharves. However, fishing ports are usually located in semi-enclosed seas, leading to the accumulation of land-based pollution in port environments. Fishing ports are known potential sinks for land-sourced pollutants, such as heavy metals, phthalates, polycyclic aromatic hydrocarbons, and petroleum hydrocarbons. Currently, comprehensive research on the distribution and ecological risk of heavy metals in fishing ports is very limited. With no environmental and scientific data available for reference, it is difficult to formulate appropriate pollution control and prevention strategies for fishing ports. Environmental risk assessment in aquatic ecosystems typically uses biomarkers to detect interactions between potential hazards and biological systems. Next to knowing environmental contaminant levels in tissues and the environment, it is important to link to potentially deleterious effects at higher levels of biological organization, such as biochemistry, physiology, and overall health status. Biochemical reactions are frequently used as biomarkers in sentinel model species sampled from reference sites, for monitoring xenobiotic pollution in coastal areas. However, multiple biomarkers were too complex and could not directly reflect the toxic effects of pollutants on organisms, while the integrated biomarker response (IBR) index could overcome this and comprehensively evaluate the aquatic ecosystem health status.The primary purpose of this study was to evaluate the overall pollution level and risks in fishing ports. Samples of green mussels (Perna viridis) and surface water were collected at 12 sampling points in four fishing ports located in Guangdong and Guangxi provinces, China. Six types of heavy metals were measured in the surface water and soft tissues of P. viridis by inductively coupled plasma mass spectrometry. Moreover, biomarkers of the antioxidant defense system, such as superoxide dismutase (SOD), glutathione peroxidase (GPx), catalase (CAT), and malondialdehyde (MDA), were analyzed in the hepatopancreas of P. viridis to calculate the IBR index. The results showed that the range of concentrations of Cu, Zn, Pb, Cd, As, and Cr in seawater was 1.13–2.37, 6.67–33.43, 0.14–0.32, 0.03–0.32, 1.09–1.73, and 0.80–1.20 μg/L, respectively, while in the soft tissues of P. viridis, it was 8.31–11.93, 67.92–103.17, 0.88–3.07, 0.80–2.33, 9.61–12.70, and 2.54–4.75 mg/kg, respectively. The mean concentrations of Cu, Zn, Pb, Cd, As, and Cr in each fishing port were lower than the fourth grade of the National Seawater Quality Standard (GB 3097-1997). The concentrations of heavy metals in the surface water and soft tissues of P. viridis were generally at a low level, the comprehensive pollution indices (PI) of heavy metals in the surface water of all four fishing ports were within the natural background range, and the comprehensive pollution indices (Pin) of heavy metals in the soft tissues of P. viridis were in the no pollution category. The PI of heavy metals in the surface water was Shekou Port > Nanwan Port > Dahao Port > Yuwan Port, while the Pin of heavy metals in the soft tissues of P. viridis was Yuwan Port > Shekou Port > Nanwan Port > Dahao Port. In addition, Cu concentrations in both the surface water and soft tissues of P. viridis from Shekou Port were the highest among those from the four fishing ports. Furthermore, there was no significant difference in MDA content or SOD, CAT, and GPx enzyme activities, in the hepatopancreas of P. viridis from the four fishing ports. The IBR index of P. viridis was 4.50 in Shekou Port, 2.14 in Yuwan Port, 1.91 in Dahao Port, and 1.50 in Nanwan Port, which showed a decreasing trend from Shekou Port > Yuwan Port > Dahao Port > Nanwan Port. The highest IBR index was identified at Shekou Port, which agreed with the profiles of the comprehensive pollution index of seawater. According to the correlation analysis, the IBR index showed no significant correlation with the comprehensive pollution index of seawater and marine mussels. It was noteworthy that the IBR index displayed significant positive correlations with Cu concentrations in seawater and mussel tissues, which indicated that Cu pollution may be an important factor to consider in pollution assessments of fishing ports.Overall, this study provides the first evidence of using the IBR index to evaluate the heavy metal pollution status of fishing ports. The pollution level and potential risk of heavy metals in Shekou Port were higher than those of the other three fishing ports. The IBR index coupled with chemical analysis is useful to assess the environmental pollution status of fishing ports for pollution source control and management policy formulation