deepAMPNet: a novel antimicrobial peptide predictor employing AlphaFold2 predicted structures and a bi-directional long short-term memory protein language model.

Background: Global public health is seriously threatened by the escalating issue of antimicrobial resistance (AMR). Antimicrobial peptides (AMPs), pivotal components of the innate immune system, have emerged as a potent solution to AMR due to their therapeutic potential. Employing computational methodologies for the prompt recognition of these antimicrobial peptides indeed unlocks fresh perspectives, thereby potentially revolutionizing antimicrobial drug development. Methods: In this study, we have developed a model named as deepAMPNet. This model, which leverages graph neural networks, excels at the swift identification of AMPs. It employs structures of antimicrobial peptides predicted by AlphaFold2, encodes residue-level features through a bi-directional long short-term memory (Bi-LSTM) protein language model, and constructs adjacency matrices anchored on amino acids' contact maps. Results: In a comparative study with other state-of-the-art AMP predictors on two external independent test datasets, deepAMPNet outperformed in accuracy. Furthermore, in terms of commonly accepted evaluation matrices such as AUC, Mcc, sensitivity, and specificity, deepAMPNet achieved the highest or highly comparable performances against other predictors. Conclusion: deepAMPNet interweaves both structural and sequence information of AMPs, stands as a high-performance identification model that propels the evolution and design in antimicrobial peptide pharmaceuticals. The data and code utilized in this study can be accessed at https://github.com/Iseeu233/deepAMPNet.

Genome-Wide Identification and Characterization of CCT Gene Family from Microalgae to Legumes.

The CCT (CO, COL and TOC1) gene family has been elucidated to be involved in the functional differentiation of the products in various plant species, but their specific mechanisms are poorly understood. In the present investigation, we conducted a genome-wide identification and phylogenetic analysis of CCT genes from microalgae to legumes. A total of 700 non-redundant members of the CCT gene family from 30 species were identified through a homology search. Phylogenetic clustering with Arabidopsis and domain conservation analysis categorized the CCT genes into three families. Multiple sequence alignment showed that the CCT domain contains important amino acid residues, and each CCT protein contains 24 conserved motifs, as demonstrated by the motif analysis. Whole-genome/segment duplication, as well as tandem duplication, are considered to be the driving forces in the evolutionary trajectory of plant species. This comprehensive investigation into the proliferation of the CCT gene family unveils the evolutionary dynamics whereby WGD/segment duplication is the predominant mechanism contributing to the expansion of the CCT genes. Meanwhile, the examination of the gene expression patterns revealed that the expression patterns of CCT genes vary in different tissues and at different developmental stages of plants, with high expression in leaves, which is consistent with the molecular regulation of flowering in photosynthesis by CCT. Based on the protein-protein interaction analysis of CCT genes in model plants, we propose that the CCT gene family synergistically regulates plant development and flowering with light-signaling factors (PHYs and PIFs) and MYB family transcription factors. Understanding the CCT gene family's molecular evolution enables targeted gene manipulation for enhanced plant traits, including optimized flowering and stress resistance.

Potential xylose transporters regulated by CreA improved lipid yield and furfural tolerance in oleaginous yeast Saitozyma podzolica zwy-2-3.

Lignocellulose's hydrolysate, a significant renewable source, contains xylose and furfural, making it challenging for industrial production of oleaginous yeast. On xylose fermentation with furfural treatment, OE::DN7263 and OE::DN7661 increased lipid yield and furfural tolerance versus WT, while, which of OE::CreA were decreased owing to CreA regulating DN7263 and DN7661 negatively. OE::CreA generated reactive oxygen species (ROS) causing oxidative damage. OE::DN7263, OE::DN7661, and ΔCreA reduced furfural via NADH; while ΔCreA produced less ROS and OE::DN7263, and OE::DN7661 scavenged ROS quickly, minimizing oxidative damage. Overall, CreA knockout increased DN7263 and DN7661 expression to facilitate xylose assimilation, enhancing NADH generation and ROS clearance. Finally, with mixed sugar fermentation, ΔCreA and OE::DN7263's biomass and lipid yield rose without furfural addition, while that of ΔCreA remained higher than WT after furfural treatment. These findings revealed how oleaginous yeast zwy-2-3 resisted furfural stress and indicated ΔCreA and OE::DN7263 might develop into robust industrial chassis strains.

Purification and characterization of a novel intracellular α-amylase with a wide variety of substrates hydrolysis and transglycosylation activity from Paenibacillus sp. SSG-1.

Intracellular α-amylase was a special glycoside hydrolase in the cytoplasm. We cloned and expressed an intracellular α-amylase, Amy, from Paenibacillus sp. SSG-1. The recombinant enzyme was purified by metal-affinity chromatography, exhibited a molecular mass of 71.7 kDa. Amy exhibited unexpectedly sequence similarity and evolutionary relationships with alpha-glucanotransferase. The docked results of Amy with maltose showed it had similar catalytic residues with α-amylase and glucanotransferase. The substrate specificity experiment showed that Amy could hydrolyze typical substrates into glucose and maltose. It was noteworthy that Amy showed the catalytic capacity of cyclomaltodextrinase and pullulanase. Meanwhile, Amy could transfer sugar molecules and form maltotetraose upon the hydrolysis of substrates. These results indicated that Amy was a novel intracellular α-amylase with distinct catalytic ability characteristics of hydrolyzing glycogen/cyclodextrin/pullulan and transglycosylation. We deduced that Amy may play an important role in utilizing maltooligosaccharides that released from extracellular α-glucan or storage α-glucan (glycogen) in Paenibacillus sp. SSG-1.

[Effects of Serum Containing Qinbai Qinfei Concentrated Pellets on Expressions of NLRP3 Inflammasome in RAW264.7 Cells Infected with Mycoplasma pneumonia].

Objective: To investigate the effects of serum containing Qinbai Qingfei concentrated pellets on expressions of NLRP3 inflammasome in RAW264. 7 cells infected with Mycoplasma pneumoniae( MP) IL-1ß. Methods: RAW264. 7 cells were randomly divided into normal group, MP model group and serum containing Qinbai Qinfei concentrated pellets group. RAW264. 7 cells and MP strain were cultured utilizing normal methods, preparation of serum containing Qinbai,with 1∶ 10 multiplicity of infection( MOI) of MP stimulation on RAW264. 7 cells; cells of each group were collected at 8,16,24 h respectively. The expressions of NLRP3,ASC and Caspase-1 mRNA were detected by the method of FQ-PCR. The expressions of NLRP3,ASC and Caspase-1 p20 protein were detected by Westernblot. The content of IL-1ß in the supernatant was measured by ELISA. Results: Compared with the normal group, he levels of NLRP3,ASC and Caspase-1 mRNA were significantly increased in the model group at 8,16,24 h respectively( P < 0. 05 or P < 0. 01); while the levels of NLRP3,ASC and Caspase-1 p20 protein were increased significantly( P < 0. 05 or P < 0. 01) at 16,24 h, and the levels of IL-1ß were increased at significantly( P < 0. 01) 24 h. Compared with the model group, the levels of NLRP3,ASC and Caspase-1 mRNA were significantly reduced in serum containing Qinbai Qinfei concentrated pellets group at 16,24 h( P < 0. 05 or P < 0. 01); the expressions of NLRP3,ASC,Caspase-1 p20 protein and the content of IL-1ß were all decreased at 24 h.Conclusion: The mechanism of antiMycoplasma pneumoniae action of Qinbai may be related to the down-regulation of NLRP3 inflammasome expressions.

Chemical constituents of Euonymus fortunei.

A new flavonol glycoside, kaempferol-3-O-ß-D-(2-O-E-p-coumaroyl)-glucopyranosyl-7-O-α-l-rhamnopyranoside (1), along with eleven known compounds including five flavonol glycosides (2-6), one phenolic glycoside (7), two megastigmane glycosides (8 and 9), two triterpenoids (10 and 11) and one alditol (12), was isolated from the aerial parts of Euonymus fortunei. Their structures were determined on the basis of spectroscopic analysis and chemical evidence. Compounds 2-4, 7, 8, and 10-12 were evaluated their antimicrobial activities against Ureaplasma urealyticumin vitro, but all tested compounds have no useful activities against Ureaplasma urealyticum.

Secretory Expression and Characterization of an Acidic Endo-Polygalacturonase Gene from Aspergillus niger SC323 in Saccharomyces cerevisiae.

The endo-polygalacturonase gene (endo-pgaA) was cloned from DNA of Aspergillus niger SC323 using the cDNA synthesized by overlapping PCR, and successfully expressed in Saccharomyces cerevisiae EBY100 through fusing the α-factor signal peptide of yeast. The full-length cDNA consists of 1,113 bp and encodes a protein of 370 amino acids with a calculated molecular mass of 38.8 kDa. After induction by galactose for 48 h, the activity of recombinant endo-PgaA in the culture supernatant can reach up to 1,448.48 U/mg. The recombinant protein was purified to homogeneity by ammonium sulfate precipitation and gel filtration column chromatography and subsequently characterized. The optimal pH and temperature of the purified recombinant enzyme were 5.0 and 50°C, respectively. The Michaelis-Menten constant (Km) and maximal velocity (Vmax) of the enzyme for pectin were 88.54 µmol/ml and 175.44 µmol/mg/min, respectively. The enzyme activity was enhanced by Ca(2+), Cu(2+), and Na(+), and strongly inhibited by Pb(2+) and Mn(2+). The pectin hydrolysates were mainly galacturonic acid and other oligo-galacturonates. Therefore, these characteristics suggest that the recombinant endo-PgaA may be of potential use in the food and feed industries.

Effects of wetland degradation on bacterial community in the Zoige Wetland of Qinghai-Tibetan Plateau (China).

Wetland degradation makes significant impacts on soil, and bacterial communities in soil are likely to respond to these impacts. The purpose of this study was to investigate the impacts of soil property, soil type and soil depth on bacterial community in different stages of soil degradation in the Zoige Wetland. Microbial biomass carbon was estimated from chloroform fumigation-extraction. Bacterial communities were evaluated by cluster and principal component analysis of DGGE banding patterns and sequencing of partial 16S rDNA PCR amplicons. Experimental results showed that microbial biomass carbon decreased with the soil types (Peat soil > Swamp soil > Meadow soil > Sandy soil) and declined with soil depths (0-20 > 20-40 > 40-60 cm). Bacterial community was affected by soil type more primarily than by soil depth. In addition, the microbial biomass carbon was strongly correlated with soil water content, soil organic carbon and total nitrogen. Sequence analysis of DGGE bands indicated that bacterial phyla of α-Proteobacteria, γ-Proteobacteria, Bacteroidetes, Flavobacterium and Unidentified bacterium predominantly existed in the soil. All these results suggest that specific changes in soil property, soil type and soil depth affected soil bacterial community both quantitatively and qualitatively.