A Bacillus velezensis strain isolated from oats with disease-preventing and growth-promoting properties.

Endophytes have been shown to promote plant growth and health. In the present study, a Bacillus velezensis CH1 (CH1) strain was isolated and identified from high-quality oats, which was capable of producing indole-3-acetic acid (IAA) and strong biofilms, and capabilities in the nitrogen-fixing and iron carriers. CH1 has a 3920 kb chromosome with 47.3% GC content and 3776 code genes. Compared genome analysis showed that the largest proportion of the COG database was metabolism-related (44.79%), and 1135 out of 1508 genes were associated with the function "biosynthesis, transport, and catabolism of secondary metabolites." Furthermore, thirteen gene clusters had been identified in CH1, which were responsible for the synthesis of fifteen secondary metabolites that exhibit antifungal and antibacterial properties. Additionally, the strain harbors genes involved in plant growth promotion, such as seven putative genes for IAA production, spermidine and polyamine synthase genes, along with multiple membrane-associated genes. The enrichment of these functions was strong evidence of the antimicrobial properties of strain CH1, which has the potential to be a biofertilizer for promoting oat growth and disease resistance.

A Multi-Omics Analysis Revealed the Diversity of the MYB Transcription Factor Family's Evolution and Drought Resistance Pathways.

The MYB transcription factor family can regulate biological processes such as ABA signal transduction to cope with drought stress, but its evolutionary mechanism and the diverse pathways of response to drought stress in different species are rarely reported. In this study, a total of 4791 MYB family members were identified in 908,757 amino acid sequences from 12 model plants or crops using bioinformatics methods. It was observed that the number of MYB family members had a linear relationship with the chromosome ploidy of species. A phylogenetic analysis showed that the MYB family members evolved in subfamily clusters. In response to drought stress, the pathways of MYB transcription factor families exhibited species-specific diversity, with closely related species demonstrating a higher resemblance. This study provides abundant references for drought resistance research and the breeding of wheat, soybean, and other plants.

Ubiquitous conservative interaction patterns between post-spliced introns and their mRNAs revealed by genome-wide interspecies comparison.

Introns, as important vectors of biological functions, can influence many stages of mRNA metabolism. However, in recent research, post-spliced introns are rarely considered. In this study, the optimal matched regions between introns and their mRNAs in nine model organism genomes were investigated with improved Smith-Waterman local alignment software. Our results showed that the distributions of mRNA optimal matched frequencies were highly consistent or universal. There are optimal matched frequency peaks in the UTR regions, which are obvious, especially in the 3'-UTR. The matched frequencies are relatively low in the CDS regions of the mRNA. The distributions of the optimal matched frequencies around the functional sites are also remarkably changed. The centers of the GC content distributions for different sequences are different. The matched rate distributions are highly consistent and are located mainly between 60% and 80%. The most probable value of the optimal matched segments is about 20 bp for lower eukaryotes and 30 bp for higher eukaryotes. These results show that there are abundant functional units in the introns, and these functional units are correlated structurally with all kinds of sequences of mRNA. The interaction between the post-spliced introns and their corresponding mRNAs may play a key role in gene expression.

A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA.

Studies have shown that post-spliced introns promote cell survival when nutrients are scarce, and intron loss/gain can influence many stages of mRNA metabolism. However, few approaches are currently available to study the correlation between intron sequences and their corresponding mature mRNA sequences. Here, based on the results of the improved Smith-Waterman local alignment-based algorithm method (SW method) and binding free energy weighted local alignment algorithm method (BFE method), the optimal matched segments between introns and their corresponding mature mRNAs in Caenorhabditis elegans (C.elegans) and their relative matching frequency (RF) distributions were obtained. The results showed that although the distributions of relative matching frequencies on mRNAs obtained by the BFE method were similar to the SW method, the interaction intensity in 5'and 3'untranslated regions (UTRs) regions was weaker than the SW method. The RF distributions in the exon-exon junction regions were comparable, the effects of long and short introns on mRNA and on the five functional sites with BFE method were similar to the SW method. However, the interaction intensity in 5'and 3'UTR regions with BFE method was weaker than with SW method. Although the matching rate and length distribution shape of the optimal matched fragment were consistent with the SW method, an increase in length was observed. The matching rates and the length of the optimal matched fragments were mainly in the range of 60%-80% and 20-30bp, respectively. Although we found that there were still matching preferences in the 5'and 3'UTR regions of the mRNAs with BFE, the matching intensities were significantly lower than the matching intensities between introns and their corresponding mRNAs with SW method. Overall, our findings suggest that the interaction between introns and mRNAs results from synergism among different types of sequences during the evolutionary process.

Identification of Disease-Related 2-Oxoglutarate/Fe (II)-Dependent Oxygenase Based on Reduced Amino Acid Cluster Strategy.

The 2-oxoglutarate/Fe (II)-dependent (2OG) oxygenase superfamily is mainly responsible for protein modification, nucleic acid repair and/or modification, and fatty acid metabolism and plays important roles in cancer, cardiovascular disease, and other diseases. They are likely to become new targets for the treatment of cancer and other diseases, so the accurate identification of 2OG oxygenases is of great significance. Many computational methods have been proposed to predict functional proteins to compensate for the time-consuming and expensive experimental identification. However, machine learning has not been applied to the study of 2OG oxygenases. In this study, we developed OGFE_RAAC, a prediction model to identify whether a protein is a 2OG oxygenase. To improve the performance of OGFE_RAAC, 673 amino acid reduction alphabets were used to determine the optimal feature representation scheme by recoding the protein sequence. The 10-fold cross-validation test showed that the accuracy of the model in identifying 2OG oxygenases is 91.04%. Besides, the independent dataset results also proved that the model has excellent generalization and robustness. It is expected to become an effective tool for the identification of 2OG oxygenases. With further research, we have also found that the function of 2OG oxygenases may be related to their polarity and hydrophobicity, which will help the follow-up study on the catalytic mechanism of 2OG oxygenases and the way they interact with the substrate. Based on the model we built, a user-friendly web server was established and can be friendly accessed at http://bioinfor.imu.edu.cn/ogferaac.

Potential relations between post-spliced introns and mature mRNAs in the Caenorhabditis elegans genome.

There are potential interactions between introns and their corresponding coding sequences (CDSs) in ribosomal protein genes that have been proposed by our group and the interactions are achieved by sequence matches between the two kinds of sequences. Here, the optimal matching relations between mature mRNAs and their corresponding introns in Caenorhabditis elegans (C.elegans) were investigated by improved Smith-Waterman local alignment software. Our results showed that the remarkably matched regions appear in the untranslated regions (UTRs) of mRNAs, especially in the 3' UTR. The optimal matched segments (OMSs) are highly organized segments. In addition, the optimal matching relations were analysed between mature mRNAs and other introns. The matching strengths in the UTRs are clearly lower than those in their corresponding introns. Our studies indicate that there are potential interactions between mature mRNAs and their corresponding introns and the post-spliced introns should have other novel functions in the gene expression process.

Evolutionary analysis of nucleosome positioning sequences based on New Symmetric Relative Entropy.

New Symmetric Relative Entropy (NSRE) was applied innovatively to analyze the nucleosome sequences in S. cerevisiae, S. pombe and Drosophila. NSRE distributions could well reflect the characteristic differences of nucleosome sequences among three organisms, and the differences indicate a concerted evolution in the sequence usage of nucleosome. Further analysis about the nucleosomes around TSS shows that the constitutive property of +1/-1 nucleosomes in S. cerevisiae is different from that in S. pombe and Drosophila, which indicates that S. cerevisiae has a different transcription regulation mechanism based on nucleosome. However, in either case, the nucleosome dyad region is conserved and always has a higher NSRE. Base composition analysis shows that this conservative property in nucleosome dyad region is mainly determined by base A and T, and the dependence degrees on base A and T are consistent in three organisms.

The evolution mechanism of intron length.

Within two years of their discovery in 1977, introns were found to have a positive effect on gene expression. Our result shows that introns can achieve gene expression and regulation through interaction with corresponding mRNA sequences. On the base of Smith-Waterman method, local comparing helps us get the optimal matched segments between intron sequences and mRNA sequences. Studying the distribution regulation of the optimal matching region on intron sequences of ribosomal protein genes about 27 species, we find that the intron length evolution processes beginning from 5' end to 3' end and increasing one by one structural unit, which comes up with a possible mechanism for the intron length evolution. The intron of structure units is conservative with about 60bp length, but the length of linker sequence between structure units changes a lot. Interestingly, distributions of the length and matching rate of optimal matched segments are consistent with sequence features of miRNA and siRNA. These results indicate that the interaction between intron sequences and mRNA sequences is a kind of functional RNA-RNA interaction. Meanwhile, the two kinds of sequences above are co-evolved and interactive to play their functions.

[Preparation and luminescence properties of nanomaterials TiO2-SiO2 doped with Eu3+].

In the present paper, the samples of nanomaterials TiO2-SiO2:Eu3+ with different proportion of Ti/Si were prepared with the sol-gel method, and influence of the proportion of Ti/Si on the luminescence properties of samples have was studied. The structure of the samples was examined by FTIR, indicating that the compound TiO2 and SiO2 reacted, forming the new chemical bond of Ti-O-Si. The TEM of samples show that TiO2-SiO2:Eu3+ are sphericity nanoparticles with monodispersion and uniform size of 35 nm. The samples were still anatase phase after annealing at 900 degrees C, which was studied by XRD and SAED, suggesting that the bond of Ti-O-Si was conducive to the stability of anatase phase. There will be isoelectronic trap as Si4+ enters the TiO2 lattice replacing some of the Ti4+ position, and this structure is conducive to transfering energy and improving the transition of Eu3+ (7F0 --> 5D2), which were found by excitation and emission spectra.

[Preparation and luminescent properties of CaMoO4:Tb3+].

The precursor of the sample CaMoO4:Tb3+ was prepared by the coprecipitation method. TG-DTA spectra show that there is, at 850 degrees C, an energy absorption peak, suggesting that the sample reaches the activation spot of its response. The XRD pattern of the roasted sample shows that CaMoO4:Tb3+, in the single phase, is a representative scheelite structure of CaMoO4, but the peaks shift toward right, implying that tiny crystal defect in the crystal is produced. The defect is likely to be formed by the formation of the holes as two Tb3+ replace three Ca2+ in a cell. The excitation and emission spectra of the sample were investigated and revealed that the defect structure of the sample is in favor of the energy transfer of the characteristic peak (488 nm) of the MoO4(2-) effectively to Tb3+, and makes the 4f electrons of the Tb3+ transit, especially the (7)F6-->(5)D4 electronic transition (488 nm) of the Tb3+, to be greatly strengthened. As a result, the emission spectra with lamdaex=488 nm show that the emission intensity of the spontaneously activated fluorescence MoO4(2-) is greatly weakened, while the green light luminescence intensity of the (5)D4-->(7)F5 transition (544 nm) of the Tb3+ is greatly enhanced. This suggests that the sample CaMoO4:Tb3+ will become the luminescence material with potentially great application value.