Machine Learning Aided Design and Optimization of Thermal Metamaterials.

Artificial Intelligence (AI) has advanced material research that were previously intractable, for example, the machine learning (ML) has been able to predict some unprecedented thermal properties. In this review, we first elucidate the methodologies underpinning discriminative and generative models, as well as the paradigm of optimization approaches. Then, we present a series of case studies showcasing the application of machine learning in thermal metamaterial design. Finally, we give a brief discussion on the challenges and opportunities in this fast developing field. In particular, this review provides: (1) Optimization of thermal metamaterials using optimization algorithms to achieve specific target properties. (2) Integration of discriminative models with optimization algorithms to enhance computational efficiency. (3) Generative models for the structural design and optimization of thermal metamaterials.

Fucoxanthin from marine microalgae: A promising bioactive compound for industrial production and food application.

Fucoxanthin attracts increasing attentions due to its potential health benefits, which has been exploited in several food commodities. However, fucoxanthin available for industrial application is mainly derived from macroalgae, and is not yet sufficiently cost-effective compared with microalgae. This review focuses on the strategies to improve fucoxanthin productivity and approaches to reduce downstream costs in microalgal production. Here we comprehensively and critically discuss ways and methods to increase the cell growth rate and fucoxanthin content of marine microalgae, including strain screening, condition optimization, design of culture mode, metabolic and genetic engineering, and scale-up production of fucoxanthin. The approaches in downstream processes provide promising alternatives for fucoxanthin production from marine microalgae. Besides, this review summarizes fucoxanthin improvements in solubility and bioavailability by delivery system of emulsion, nanoparticle, and hydrogel, and discusses fucoxanthin metabolism with gut microbes. Fucoxanthin production from marine microalgae possesses numerous advantages in environmental sustainability and final profits to meet incremental global market demands of fucoxanthin. Strategies of adaptive evolution, multi-stage cultivation, and bioreactor improvements have tremendous potentials to improve economic viability of the production. Moreover, fucoxanthin is promising as the microbiota-targeted ingredient, and nanoparticles can protect fucoxanthin from external environmental factors for improving the solubility and bioavailability.

Butyrogenic effect of galactosyl and mannosyl carbohydrates and their regulation on piglet intestinal microbiota.

Diarrhea is a global problem that causes economic losses in the pig industry. There is a growing attention on finding new alternatives to antibiotics to solve this problem. Hence, this study aimed to compare the prebiotic activity of low-molecular-weight hydrolyzed guar gum (GMPS) with commercial manno-oligosaccharide (MOS) and galacto-oligosaccharide (GOS). We further identified their combined effects along with probiotic Clostridium butyricum on regulating the intestinal microbiota of diarrheal piglet by in vitro fermentation. All the tested non-digestible carbohydrates (NDCs) showed favorable short-chain fatty acid-producing activity, and GOS and GMPS showed the highest production of lactate and butyrate, respectively. After 48 h of fermentation, the greatest enhancement in the abundance of Clostridium sensu stricto 1 was observed with the combination of GMPS and C. butyricum. Notably, all the selected NDCs significantly decreased the abundances of pathogenic bacteria genera Escherichia-Shigella and Fusobacterium and reduced the production of potentially toxic metabolites, including ammonia nitrogen, indole, and skatole. These findings demonstrated that by associating with the chemical structure, GMPS exhibited butyrogenic effects in stimulating the proliferation of C. butyricum. Thus, our results provided a theoretical foundation for further application of galactosyl and mannosyl NDCs in the livestock industry. KEY POINTS: • Galactosyl and mannosyl NDCs showed selective prebiotic effects. • GMPS, GOS, and MOS reduced pathogenic bacteria and toxic metabolites production. • GMPS specifically enhanced the Clostridium sensu stricto 1 and butyrate production.

Genome analysis and 2'-fucosyllactose utilization characteristics of a new Akkermansia muciniphila strain isolated from mice feces.

Akkermansia muciniphila is considered to be a next-generation probiotic, and closely related to host metabolism and immune response. Compared with other probiotics, little is known about its genomic analysis. Therefore, further researches about isolating more A. muciniphila strains and exploring functional genes are needed. In the present study, a new strain isolated from mice feces was identified as A. muciniphila (MucX). Whole-genome sequencing and annotation revealed that MucX possesses key genes necessary for human milk oligosaccharides (HMO) utilization, including α-L-fucosidases, ß-galactosidases, exo-α-sialidases, and ß-acetylhexosaminidases. The complete metabolic pathways for γ-aminobutyric acid and squalene and genes encoding functional proteins, such as the outer membrane protein Amuc_1100, were annotated in the MucX genome. Comparative genome analysis was used to identify functional genes unique to MucX compared to six other A. muciniphila strains. Results showed MucX genome possesses unique genes, including sugar transporters and transferases. Single-strain incubation revealed faster utilization of 2'-fucosyllactose (2'-FL), galacto-oligosaccharides, and lactose by MucX than by A. muciniphila DSM 22959. This study isolated and identified an A. muciniphila strain that can utilize 2'-FL, and expolored the genes related to HMO utilization and special metabolites, which provided a theoretical basis for the further excavation of A. muciniphila function and the compound application with fucosylated oligosaccharides.

Complete-genome sequence and in vitro probiotic characteristics analysis of Bifidobacterium pseudolongum YY-26.

AIMS: The aim was to isolate a neotype bifidobacteria strain and evaluate its in vitro probiotic potential. METHODS AND RESULTS: Bifidobacterium pseudolongum YY-26 (CGMCC 24310) was isolated from faeces of mice treated with low-molecular-weight hydrolyzed guar gum (GMPS) and identified based on 16S rRNA sequence and genome sequence. Whole-genome sequencing obtained using PacBio's single-molecular and Illumina's paired-end sequencing technology. A genome of 2.1 Mb in length, with 1877 predicted protein-coding sequences was obtained. Carbohydrate-Activity enZyme analysis revealed that YY-26 encodes 66 enzymes related to carbohydrate metabolism. Whole genome sequence analysis revealed the typical probiotic characteristics of YY-26, including safety in genetic level and ability to produce beneficial metabolites and extracellular polysaccharides. Ability of extensive carbon source utilization and short-chain fatty acid production was observed with single YY-26 cultivation. Considerable acetic acids and lactic acids were determined in GMPS utilization. YY-26 showed tolerance to simulated gastrointestinal tract and displayed appreciable antioxidant activity of free radical scavenging. CONCLUSIONS: B. pseudolongum YY-26 was identified with numerous probiotic-associated genes and its probiotic characteristics were verified in vitro. SIGNIFICANCE AND IMPACT OF STUDY: This study supplemented with limited publicly information regarding the genomes of B. pseudolongum strains and revealed the probiotic potential of YY-26.

Response mechanism of Vibrio parahaemolyticus at high pressure revealed by transcriptomic analysis.

Vibrio parahaemolyticus is a common pathogen in aquatic products, such as shellfishes. Laboratory-based simulated studies demonstrated that V. parahaemolyticus can tolerate high hydrostatic pressure (HHP) up to 20 MPa. However, the molecular mechanisms of high-pressure adaptation remain unclear. Herein, we analyzed the physiological changes and transcriptomic responses of V. parahaemolyticus ATCC 17,802 under HHP conditions to determine the possible survival mechanisms. Under HHP conditions, the morphology of V. parahaemolyticus was notably changed exhibiting the coccoid microbial cells. The transcriptome analysis revealed that there were 795 differentially expressed genes (DEGs) under the 20 MPa condition, including 406 upregulated DEGs and 389 downregulated DEGs. Most of the downregulated DEGs encoded proteins related to energy metabolism, such as citrate synthase (gltA), pyruvate kinase (pyk), and glyceraldehyde-3-phosphate dehydrogenase (gapA). Many of the upregulated DEGs encoded proteins related to adhesion and virulence factors, such as RNA polymerase σ factor (rpoE), L-threonine 3-dehydrogenase, and bacterial nucleotide signal c-di-GMP (WU75_RS02745 and WU75_RS07185). In our proposed mechanism model, V. parahaemolyticus responds to HHP stress through RNA polymerase σ factor RpoE. These findings indicate that V. parahaemolyticus cells may adopt a complex adaptation strategy to cope with HHP stress. KEY POINTS: •The transcriptomic response of Vibrio parahaemolyticus under HHP conditions was studied for the first time. •V. parahaemolyticus may adopt a complex adaptation strategy to cope with HHP stress. •ToxRS and RpoE played an important role in sensing and responding the HHP signal.

Regulation of Virulence Factors Expression During the Intestinal Colonization of Vibrio parahaemolyticus.

Colonization and adhesion are the key steps for Vibrio parahaemolyticus to infect human body and cause seafood poisoning. However, at present, there is a lack of systematic review on the regulation of virulence factors expression during the intestinal colonization of V. parahaemolyticus. This review aims to describe the virulence factors associated with the colonization and adhesion of V. parahaemolyticus (multivalent adhesion molecule 7, enolase secretion, use of flagella, biofilm formation, and the action of secretion systems) and focuses on the aspects that affect these processes in V. parahaemolyticus, including secretion systems, quorum sensing (QS), and the human gastrointestinal tract. V. parahaemolyticus regulates the expression of virulence factors by forming a virulence regulation network through QS and the core regulator, ToxR, which contributes to the early colonization of the pathogen. In the virulence regulation network, the secretion systems, type III and type VI secretion systems, help V. parahaemolyticus adhere to the distal end of the small intestine by secreting effectors that induce the lysis of epithelial cells and change the shape of the intestinal lining, which provides nutrients and a suitable environment for its growth. This review summarizes the research progress in recent years on the virulence factors associated with the colonization and adhesion of V. parahaemolyticus, which provides valuable information for the safety control of marine food.

Characterization of Recombinant Antimicrobial Peptide BMGlv2 Heterologously Expressed in Trichoderma reesei.

Antimicrobial peptides (AMPs) serve as alternative candidates for antibiotics and have attracted the attention of a wide range of industries for various purposes, including the prevention and treatment of piglet diarrhea in the swine industry. Escherichia coli, Salmonella, and Clostridium perfringens are the most common pathogens causing piglet diarrhea. In this study, the antimicrobial peptide gloverin2 (BMGlv2), derived from Bombyx mandarina, was explored to determine the efficient prevention effect on bacterial piglet diarrhea. BMGlv2 was heterologously expressed in Trichoderma reesei Tu6, and its antimicrobial properties against the three bacteria were characterized. The results showed that the minimum inhibitory concentrations of the peptide against E. coli ATCC 25922, S. derby ATCC 13076, and C. perfringens CVCC 2032 were 43.75, 43.75, and 21.86 µg/mL, respectively. The antimicrobial activity of BMGlv2 was not severely affected by high temperature, salt ions, and digestive enzymes. It had low hemolytic activity against rabbit red blood cells, indicating its safety for use as a feed additive. Furthermore, the measurements of the leakage of bacterial cell contents and scanning electron microscopy of C. perfringens CVCC 2032 indicated that BMGlv2 exerted antimicrobial activity by destroying the cell membrane. Overall, this study showed the heterologous expression of the antimicrobial peptide BMGlv2 in T. reesei and verified its antimicrobial properties against three common pathogenic bacteria associated with piglet diarrhea, which can provide a reference for the applications of AMPs as an alternative product in industrial agriculture.

Application of Microalgal Stress Responses in Industrial Microalgal Production Systems.

Adaptive laboratory evolution (ALE) has been widely utilized as a tool for developing new biological and phenotypic functions to explore strain improvement for microalgal production. Specifically, ALE has been utilized to evolve strains to better adapt to defined conditions. It has become a new solution to improve the performance of strains in microalgae biotechnology. This review mainly summarizes the key results from recent microalgal ALE studies in industrial production. ALE designed for improving cell growth rate, product yield, environmental tolerance and wastewater treatment is discussed to exploit microalgae in various applications. Further development of ALE is proposed, to provide theoretical support for producing the high value-added products from microalgal production.

A thermostable glucose oxidase from Aspergillus heteromophus CBS 117.55 with broad pH stability and digestive enzyme resistance.

In this study, the heterologous expression of an engineered thermostablle glucose oxidase from Aspergillus heteromophus CBS 117.55 was achieved in P. pastoris. This recombinant GoxAh was thermostable, with an optimal temperature range 25 °C-65 °C, and it was capable of retaining greater than 90% of its initial activity following a 10-min incubation at 75 °C. This enzyme had an optimum pH of 6.0, and it could retain above 80% of its initial activity following a 2-h incubation at a broad pH range (2.0-8.0). Moreover, GoxAh displayed excellent pepsin and trypsin resistance, and highly resistant to a range of tested metal ions and chemical reagents. These good properties make GoxAh a promising candidate for feed additive. The Km and kcat/Km values of GoxAh were 187 mM and 1.09/mM/s, which limited its widespread application to some degree. However, due to its excellent characteristics, GoxAh is still of potential economic value for high value-added areas, as well as a good initial enzyme for developing applicable feed enzyme by protein engineering.

Protective effects of enzyme degradation extract from Porphyra yezoensis against oxidative stress and brain injury in D-galactose-induced ageing mice.

The present study investigated the effects of Porphyra yezoensis enzyme degradation extract (PYEDE) on the brain injuries and neurodegenerative diseases due to oxidative stress. We used in vitro antioxidant systems to verify the antioxidant potential of PYEDE. The results indicated that the PYEDE alleviated weight loss and organ atrophy, reduced the levels of lipid peroxidation and protein carbonylation and elevated reduced glutathione (GSH) content in the serum and brains of the d-galactose-induced ageing model mice. The PYEDE also renewed the glutathione peroxidase (GSH-Px), superoxide dismutase and total antioxidant capability activities, down-regulated the inducible nitric oxide synthase activity and nitric oxide levels, normalised the hippocampal neurons and modulated multiple neurotransmitter systems by inhibiting the activities of acetylcholinesterase and monoamine oxidase in the up-regulation of acetylcholine, dopamine and noradrenaline levels. Overall, the PYEDE is a promising supplement for the alleviation of oxidative stress and age-associated brain diseases.

Determination of the Extraction, Physicochemical Characterization, and Digestibility of Sulfated Polysaccharides in Seaweed-Porphyra haitanensis.

The aim of the study was to extract Porphyra haitanensis polysaccharides (PHPs) using the water extraction and alcohol precipitation methods and explore their antioxidant activity and physicochemical properties. The single-factor and Box-Behnken response surface methodologies were used to optimize the extraction of polysaccharides from Porphyra haitanensis. Our results showed that the polysaccharide yield was as high as 20.48% with a raw material to water ratio of 0.04, and extraction time of 3 h at 80 °C. The extraction rate observed was similar to the actual extraction rate, thus proving the reliability of the optimization model. The extracted polysaccharides primarily consisted of galactose, glucose, and fucose in the molar ratio 76.2:2.1:1, respectively. The high performance gel permeation chromatography (HPGPC) results showed that the molecular weight of the PHPs obtained was 6.3 × 105 Da, and the sulfate content was 2.7 mg/mL. Fourier infrared spectroscopy was used to analyze the functional groups and structures of the polysaccharides. The effect of concentration, temperature, and pH on the apparent viscosity of the PHPs solution were studied using rheology experiments, which revealed that PHPs were a "non-Newtonian fluid" with shear-thinning behavior. The viscosity of the PHPs gradually increased with increasing sugar concentration, and decreased with increasing temperature, acidity, and alkalinity. Detection of the antioxidant activity of OH*, DPPH*, and ABTS* revealed that the scavenging activity of ABTS* was higher than that of OH* and DPPH* in the concentration range of 1-5 mg/mL. In the experiments of simulating gastric juice and alpha amylase in vitro, it was found that PHPs can better resist digestion of alpha amylase, and have better resistance than fructooligosaccharide (FOS), so PHPs have potential prebiotic activity. These findings demonstrate the potential of PHPs for use in the food and cosmetic industries.

Expression and Characterization of an Alginate Lyase and Its Thermostable Mutant in Pichia pastoris.

Alginate is one of the most abundant polysaccharides in algae. Alginate lyase degrades alginate through a ß-elimination mechanism to produce alginate oligosaccharides with special bioactivities. Improving enzyme activity and thermal stability can promote the application of alginate lyase in the industrial preparation of alginate oligosaccharides. In this study, the recombinant alginate lyase cAlyM and its thermostable mutant 102C300C were expressed and characterized in Pichia pastoris. The specific activities of cAlyM and 102C300C were 277.1 U/mg and 249.6 U/mg, respectively. Both enzymes showed maximal activity at 50 °C and pH 8.0 and polyG preference. The half-life values of 102C300C at 45 °C and 50 °C were 2.6 times and 11.7 times the values of cAlyM, respectively. The degradation products of 102C300C with a lower degree of polymerization contained more guluronate. The oligosaccharides with a polymerization degree of 2-4 were the final hydrolytic products. Therefore, 102C300C is potentially valuable in the production of alginate oligosaccharides with specific M/G ratio and molecular weights.

Lipase is associated with deltamethrin resistance in Culex pipiens pallens.

The wide application of pyrethroids has led to the rapid development of insecticide resistance in mosquitoes, leading to a rise in mosquito-borne diseases. We previously identified five differentially expressed lipase family genes upon evaluating the transcriptomes of deltamethrin-resistant and deltamethrin-susceptible strains of Culex pipiens pallens. Herein, the gene expression levels were verified by quantitative real-time PCR, and two lipase family genes, lipase A and pancreatic triacylglycerol lipase A, were chosen for further investigations. Using cell viability assays and Centers for Disease Control and Prevention bottle bioassays, lipase A was found to increase the resistance of mosquitoes against deltamethrin both in vitro and in vivo. Our findings indicate that lipase A is involved in conferring deltamethrin resistance in Cx. pipiens pallens.

Identification and classification of differentially expressed genes in pyrethroid-resistant Culex pipiens pallens.

Culex pipiens pallens is an important vector that transmits Bancroftian filariasis, Japanese encephalitis and other diseases that pose a serious threat to human health. Extensive and improper use of insecticides has caused insecticide resistance in mosquitoes, which has become an important obstacle to the control of mosquito-borne diseases. It is crucial to investigate the underlying mechanism of insecticide resistance. The aims of this study were to identify genes involved in insecticide resistance based on the resistance phenotype, gene expression profile and single-nucleotide polymorphisms (SNPs) and to screen for major genes controlling insecticide resistance. Using a combination of SNP and transcriptome data, gene expression quantitative trait loci (eQTLs) were studied in deltamethrin-resistant mosquitoes. The most differentially expressed pathway in the resistant group was identified, and a regulatory network was built using these SNPs and the differentially expressed genes (DEGs) in this pathway. The major candidate genes involved in the control of insecticide resistance were analyzed by qPCR, siRNA microinjection and CDC bottle bioassays. A total of 85 DEGs that encoded putative detoxification enzymes (including 61 P450s) were identified in this pathway. The resistance regulatory network was built using SNPs, and these metabolic genes, and a major gene, CYP9AL1, were identified. The functional role of CYP9AL1 in insecticide resistance was confirmed by siRNA microinjection and CDC bottle bioassays. Using the eQTL approach, we identified important genes in pyrethroid resistance that may aid in understanding the mechanism underlying insecticide resistance and in targeting new measures for resistance monitoring and management.

Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria.

Nondigestible carbohydrates (NDCs) are fermentation substrates in the colon after escaping digestion in the upper gastrointestinal tract. Among NDCs, resistant starch is not hydrolyzed by pancreatic amylases but can be degraded by enzymes produced by large intestinal bacteria, including clostridia, bacteroides, and bifidobacteria. Nonstarch polysaccharides, such as pectin, guar gum, alginate, arabinoxylan, and inulin fructans, and nondigestible oligosaccharides and their derivatives, can also be fermented by beneficial bacteria in the large intestine. Butyrate is one of the most important metabolites produced through gastrointestinal microbial fermentation and functions as a major energy source for colonocytes by directly affecting the growth and differentiation of colonocytes. Moreover, butyrate has various physiological effects, including enhancement of intestinal barrier function and mucosal immunity. In this review, several representative NDCs are introduced, and their chemical components, structures, and physiological functions, including promotion of the proliferation of butyrate-producing bacteria and enhancement of butyrate production, are discussed. We also describe the strategies for achieving directional accumulation of colonic butyrate based on endogenous generation mechanisms.

TRE1 and CHS1 contribute to deltamethrin resistance in Culex pipiens pallens.

Cuticular resistance, characterized by decreased epidermal penetration, has been reported on highly pyrethroid-resistant mosquitoes. In this study, we examined the role of genes in the chitin biosynthetic pathway in the context of deltamethrin-resistant (DR) Culex pipiens pallens. We found that expression of the trehalase (TRE1) gene and chitin synthase (CHS1) gene was upregulated 1.65- and 1.75-fold with quantitative reverse transcription polymerase chain reaction, respectively, in the DR strain as compared with the deltamethrin-susceptible (DS) strain. Examination of chitin content in DR and DS pupae showed an increased amount of chitin in DR pupae. To further establish the role of TRE1 and CHS1 in deltamethrin resistance, we injected mosquitoes with small interfering RNA (siRNA) for knockdown of TRE1 or CHS1 expression. The mortality rates of DR mosquitoes exposed to insecticides increased 17% and 26% after siTRE1 and siCHS1 injection, respectively. The siRNA treatment against TRE1 resulted in decreased expression of the downstream gene CHS1. Together, our findings support a role of TRE1 and CHS1 in the regulation of pyrethroid resistance.

Expression, Purification and Characterization of Chondroitinase AC II from Marine Bacterium Arthrobacter sp. CS01.

Chondroitinase (ChSase), a type of glycosaminoglycan (GAG) lyase, can degrade chondroitin sulfate (CS) to unsaturate oligosaccharides, with various functional activities. In this study, ChSase AC II from a newly isolated marine bacterium Arthrobacter sp. CS01 was cloned, expressed in Pichia pastoris X33, purified, and characterized. ChSase AC II, with a molecular weight of approximately 100 kDa and a specific activity of 18.7 U/mg, showed the highest activity at 37 °C and pH 6.5 and maintained stability at a broad range of pH (5⁻7.5) and temperature (below 35 °C). The enzyme activity was increased in the presence of Mn2+ and was strongly inhibited by Hg2+. Moreover, the kinetic parameters of ChSase AC II against CS-A, CS-C, and HA were determined. TLC and ESI-MS analysis of the degradation products indicated that ChSase AC II displayed an exolytic action mode and completely hydrolyzed three substrates into oligosaccharides with low degrees of polymerization (DPs). All these features make ChSase AC II a promising candidate for the full use of GAG to produce oligosaccharides.

Carbonic anhydrase II confers resistance to deltamethrin in Culex pipiens pallens.

Carbonic anhydrases (CAs) are metabolic enzymes that regulate the physiological equilibrium in a variety of organisms. In this study, we investigated the function of CA II in Culex pipiens pallens using real-time quantitative polymerase chain reaction and double-stranded RNA injection. CA II transcripts were more abundant in the deltamethrin-susceptible strain than the deltamethrin-resistant strain. The activities of metabolic enzymes increased when the CA II expression was silenced. These findings suggest CA II regulates deltamethrin resistance by altering metabolic enzyme activity, and could serve as a potential genetic marker for monitoring deltamethrin resistance in mosquitoes.

piRNA-3878 targets P450 (CpCYP307B1) to regulate pyrethroid resistance in Culex pipiens pallens.

Piwi-interacting RNAs (piRNAs) are a novel class of noncoding single-strand RNAs. They play an important role in the germ cell maintenance, brain development, epigenetic regulation of cancer, and antiviral function. However, little is known about the relationship between the piRNAs and insecticide resistance in mosquitoes. In this study, we reported that piRNA-3878 was related with pyrethroid resistance in Culex pipiens pallens. The expression level of piRNA-3878 was lower in both laboratory and field-collected deltamethrin-resistant (DR) strains. Overexpression of piRNA-3878 increased the susceptibility of the DR strain, while inhibiting the expression of piRNA-3878 in DS strain made the mosquitoes more resistant to deltamethrin. Furthermore, we identified that CpCYP307B1 was the target of piRNA-3878. The mosquito mortality rate was increased after downregulating the expression of CpCYP307B1. These findings revealed that piRNA-3878 could target CpCYP307B1 to regulate pyrethroid resistance.