Molecular insights into the catabolism of dibutyl phthalate in Pseudomonas aeruginosa PS1 based on biochemical and multi-omics approaches.

A comprehensive understanding of the molecular mechanisms underlying microbial catabolism of dibutyl phthalate (DBP) is still lacking. Here, we newly isolated a bacterial strain identified as Pseudomonas aeruginosa PS1 with high efficiency of DBP degradation. The degradation ratios of DBP at 100-1000 mg/L by this strain reached 80-99 % within 72 h without a lag phase. A rare DBP-degradation pathway containing two monobutyl phthalate-catabolism steps was proposed based on intermediates identified by HPLC-TOF-MS/MS. In combination with genomic and transcriptomic analyses, we identified 66 key genes involved in DBP biodegradation and revealed the genetic basis for a new complete catabolic pathway from DBP to Succinyl-CoA or Acetyl-CoA in the genus Pseudomonas for the first time. Notably, we found that a series of homologous genes in Pht and Pca clusters were simultaneously activated under DBP exposure and some key intermediate degradation related gene clusters including Pht, Pca, Xyl, Ben, and Cat exhibited a favorable coexisting pattern, which contributed the high-efficient DBP degradation ability and strong adaptability to this strain. Overall, these results broaden the knowledge of the catabolic diversity of DBP in microorganisms and enhance our understanding of the molecular mechanism underlying DBP biodegradation.

Structural modification of starch and protein: From the perspective of gelatinization degree of oat flour.

To clarify the relationship between gelatinization degree and structure characteristics, oat kernels were roasted to different gelatinization degree of 15 %-90 % based on tempering water content of 22.5 %-35 %, and the structure characteristics of starch and protein were evaluated. The results showed that the increased gelatinization degree dependent on tempering water content promoted protein aggregation on the surface of starch particles, forming larger aggregates with molecular weight >100 kDa. Oat kernels presented a dense starch gel network structure induced by gelatinized starch. Partial gelatinization of starch led to a decrease in pasting viscosities (setback viscosity, 3.91 Pa·s-1.59 Pa·s) and enthalpy (5.12 J/g-0.11 J/g). With the increase of gelatinization degree, the starch crystal structure conversed from A + V type to V type, accompanied by the formation of starch-lipid complexes and a decrease of relative crystallinity (22.28 %-8.72 %). Moreover, 50 % gelatinized oat flour possessed the highest ß-sheet structure (38.04 %), but a decrease in surface hydrophobicity and an increase in endogenous fluorescence intensity were found in oat flour of gelatinization degree >50 %. This study provided a theoretical reference for the application of oat flour with different gelatinization degrees to match suitable products.

Multistable dynamics and attractors self-reproducing in a new hyperchaotic complex Lü system.

Multistable dynamics analysis of complex chaotic systems is an important problem in the field of chaotic communication security. In this paper, a new hyperchaotic complex Lü system is proposed and its basic dynamics are analyzed. Owing to the introduction of complex variables, the new system has some structurally distinctive attractors, such as flower-shaped and airfoil-shaped attractors. In addition, the evolution process of the limit cycle is also investigated. Next, the multistable coexistence behavior of the system is researched by the method of attraction basins, and the coexistence behavior of two types of hyperchaotic attractors and one type of chaotic and periodic attractors of the system are analyzed. The coexisting hyperchaotic attractors also show flower and airfoil shapes, and four types of coexistence flower-shaped attractors with different structures are perfectly explored. Moreover, the variation of coexistence attractors in the plane and space with parameters is discussed. Then, by introducing a specific piecewise function determined by a two-element method into the new high-dimensional system, the self-reproduction of the attractor can be realized to generate the multistability, and the general steps of attractors self-reproducing in the higher dimensional system are given. Finally, the circuit design of the new system is implemented, which lays a foundation for the application of complex chaotic systems.

Enhancing the quality of steamed oat cake by partially gelatinized starch in oat flour and its molecular mechanism.

The aim of this study was to investigate the effect and mechanism of partially gelatinized starch in oat flour on the rheological characteristics of the oat batter and the quality of steamed oat cakes. The results showed that an increase in the gelatinization degree of oat flour destroyed the starch granular structure and the long-range molecular order of starch, accompanied by a decrease of crystallinity from 22.28 % to 8.72 % and the formation of a starch-lipid complex. The increased gelatinization degree of oat flour destroyed the protein network and promoted the formation of the starch gel network in oat batter. Meanwhile, the addition of gelatinized oat flour enhanced the elastic behavior of the oat batter and the gas retention ability of the fermented oat batter, while decreased the total gas volume from 1075.5 mL to 827.0 mL. The steamed oat cake containing 50 % gelatinization degree of oat flour (G50) showed moderate hardness, springiness and chewiness, as well as the largest cell area fraction (37.35 %), due to the formation of a dense starch gel-protein double network and the enhancement of long/short-range molecular order of starch. Thus, this study provided the feasibility of improving the quality of oat-based fermented products by changing the gelatinization degree of oat starch.

Effects of gelatinization degree and boiling water kneading on the rheology characteristics of gluten-free oat dough.

The effects of gelatinization degree of oat flour and boiling water on the rheological characteristics of oat dough were investigated. Gelatinized oat flour had higher water absorption (2.25-3.83 g/g) and swelling (2.40-4.19), but lower solubility (6.20-8.60 %) at 25 °C. Oat dough gradually developed a honeycomb-like structure with the increase of gelatinization degree. Gelatinization treatment and boiling water kneading increased bound water content (9.39-12.89 %) and enhanced the elastic behavior of oat dough, with moderate G', lower tan δ, and higher relative elastic portion (77.40 %) and stress relaxation percentage (34.55 %) in the dough prepared by 50 % or 65 % gelatinized oat flour. Chemical interactions showed hydrogen bond and covalent bond were the main interactions in oat dough made from moderately gelatinized oat flour. Moderately gelatinization and boiling water kneading could modify the rheological characteristics and improve the texture and processing adaptability (lower adhesiveness) of oat dough.

QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study.

Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding.

Similar Bacterial Communities among Different Populations of a Newly Emerging Invasive Species, Tuta absoluta (Meyrick).

Microorganisms in the guts of insects enhance the adaptability of their hosts with different lifestyles, or those that live in different habitats. Tuta absoluta is an invasive pest that is a serious threat to tomato production in China. It has quickly spread and colonized Xinjiang, Yunnan and other provinces and regions. We used Illumina HiSeq next generation sequencing of the 16S rRNA gene to study and analyze the composition and diversity of the gut microbiota of three geographical populations of T. absoluta. At the phylum level, the most common bacteria in T. absoluta across all three geographical populations were Proteobacteria and Firmicutes. An uncultured bacterium in the Enterobacteriaceae was the dominant bacterial genus in the T. absoluta gut microbiotas. There were no significant differences in alpha diversity metrics among the Spanish, Yunnan and Xinjiang populations. The structures of the gut microbiota of the three populations were similar based on PCoA and NMDS results. The results confirmed that the microbial structures of T. absoluta from different regions were similar.

Fine-Tuning of the Grain Size by Alternative Splicing of GS3 in Rice.

Grain size is subtly regulated by multiple signaling pathways in rice. Alternative splicing is a general mechanism that regulates gene expression at the post-transcriptional level. However, to our knowledge, the molecular mechanism underlying grain size regulation by alternative splicing is largely unknown. GS3, the first identified QTL for grain size in rice, is regulated at the transcriptional and post-translational level. In this study, we identified that GS3 is subject to alternative splicing. GS3.1 and GS3.2, two dominant isoforms, accounts for about 50% and 40% of total transcripts, respectively. GS3.1 encodes the full-length protein, while GS3.2 generated a truncated proteins only containing OSR domain due to a 14 bp intronic sequence retention. Genetic analysis revealed that GS3.1 overexpressors decreased grain size, but GS3.2 showed no significant effect on grain size. Furthermore, we demonstrated that GS3.2 disrupts GS3.1 signaling by competitive occupation of RGB1. Therefore, we draw a conclusion that the alternative splicing of GS3 decreases the amount of GS3.1 and GS3.2 disrupts the GS3.1 signaling to inhibit the negative effects of GS3.1 to fine-tune grain size. Moreover, the mechanism is conserved in cereals rather than in Cruciferae, which is associated with its effects on grain size. The results provide a novel, conserved and important mechanism underlying grain size regulation at the post-transcriptional level in cereals.

Comprehensive profiling of alternative splicing landscape during secondary dormancy in oilseed rape (Brassica napus L.).

Alternative splicing is a general mechanism that regulates gene expression at the post-transcriptional level, which increases the transcriptomic diversity. Oilseed rape (Brassica napus L.), one of the main oil crops worldwide, is prone to secondary dormancy. However, how alternative splicing landscape of oilseed rape seed changes in response to secondary dormancy is unknown. Here, we analyzed twelve RNA-seq libraries from varieties "Huaiyou-SSD-V1" and "Huaiyou-WSD-H2" which exhibited high (> 95%) and low (< 5%) secondary dormancy potential, respectively, and demonstrated that alternative splicing changes led to a significant increase with the diversity of the transcripts in response to secondary dormancy induction via polyethylene glycol 6000 (PEG6000) treatment. Among the four basic alternative splicing types, intron retention dominates, and exon skipping shows the rarest frequency. A total of 8% of expressed genes had two or more transcripts after PEG treatment. Further analysis revealed that global isoform expression percentage variations in alternative splicing in differently expressed genes (DEGs) is more than three times as much as those in non-DEGs, suggesting alternative splicing change is associated with the transcriptional activity change in response to secondary dormancy induction. Eventually, 342 differently spliced genes (DSGs) associated with secondary dormancy were identified, five of which were validated by RT-PCR. The number of the overlapped genes between DSGs and DEGs associated with secondary dormancy was much less than that of either DSGs or DEGs, suggesting that DSGs and DEGs may independently regulates secondary dormancy. Functional annotation analysis of DSGs revealed that spliceosome components are overrepresented among the DSGs, including small nuclear ribonucleoprotein particles (snRNPs), serine/arginine-rich (SR) proteins, and other splicing factors. Thus, it is proposed that the spliceosome components could be exploited to reduce secondary dormancy potential in oilseed rape. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01314-8.

Functional Characterization of a Novel Heterozygous Mutation in the Glucokinase Gene That Causes MODY2 in Chinese Pedigrees.

Background: Glucokinase (GCK) plays a central role in glucose regulation. The heterozygous mutations of GCK can cause a monogenic form of diabetes, maturity-onset diabetes of the young (MODY) directly. In our study, we aimed to explore the mechanism of the novel mutation GCK p.Ala259Thr leading to glucokinase deficiency and hyperglycemia. Methods: Thirty early-onset diabetes pedigrees were referred to whole exome sequencing for novel mutations identification. Purified wild-type and mutant GCK proteins were obtained from E.coli systems and then subjected to the kinetic and thermal stability analysis to test the effects on GCK activity. Results: One novel missense mutation GCK p.Ala259Thr was identified and co-segregated with diabetes in a Chinese MODY2 pedigree. The kinetic analysis showed that this mutation result in a decreased affinity and catalytic capability for glucose. The thermal stability analysis also indicated that the mutant protein presented dramatically decreased activity at the same temperature. Conclusion: Our study firstly identified a novel MODY2 mutation p.Ala259Thr in Chinese diabetes pedigrees. The kinetic and thermal stability analysis confirmed that this mutation caused hyperglycemia through severely damaging the enzyme activities and protein stability.

Changes of aggregation and structural properties of heat-denatured gluten proteins in fast-frozen steamed bread during frozen storage.

The aim of this research was to clearly clarify the deterioration mechanism of heat-denatured gluten proteins by exploring the change of aggregation and structural characteristics of heat-denatured gluten proteins in the steamed bread system and the steamed gluten system during frozen storage. An increase in the total SDS-soluble protein content was determined, which mainly attributed to the soluble monomer protein content increased. Combined with the significant increase of free sulfhydryl, from 3.12 µmol/g to 5.06 µmol/g and 2.64 µmol/g to 3.29 µmol/g, respectively, it can be inferred that the proteins depolymerization induced by frozen storage was mainly involved in the breakdown of heat-induced glutenin-gliadin disulfide cross-linking. Frozen storage induced the conversion of random coil structure to ß-sheet structure and a ruptured microstructure with small fragment was observed. Moreover, the protein of steamed bread system was easier to depolymerize than that of the steamed gluten system.

Bacterial diversity in ballast water and sediments revealed by 2b-RAD sequencing.

Despite that the ballast water management (BWM) convention has come into force to prevent the spread of harmful aquatic organisms, to date, very few bacteria can be identified through microbial culture method. In this study, we explored a reduced-representation sequencing of 2b-RAD approach to investigate the bacterial diversity in ballast water and sediments (BWS). Our results indicated a large amount of bacteria species (1496) detected in BWS up to now, including 13 pathogens that are seriously concerning in marine environment and aquaculture like the most harmful Vibrio harveyi and Aurantimonas coralicida. We showed that the ballast water had relative lower species, which was dominated by Proteobacteria. In contrast, the sediments had richer species, which was dominated by Bacteroidetes. Although BWS differed significantly in species composition, sediments shared most of the concerned pathogens with ballast water, highlighting the importance of sediment management. In conclusion, 2b-RAD sequencing shows promise in future BWM.

Cerium-Based Metal-Organic Framework Nanocrystals Interconnected by Carbon Nanotubes for Boosting Electrochemical Capacitor Performance.

In this study, nanocrystals of a cerium-based metal-organic framework (Ce-MOF), Ce-MOF-808, are directly grown on the surface of carboxylic acid-functionalized carbon nanotubes (CNTs) by a facile one-step solvothermal synthesis method. Ce-MOF-CNT nanocomposites with various Ce-MOF-to-CNT ratios are synthesized, and their crystallinity, morphology, porosity, and electrical conductivity are examined. The redox-hopping and electrochemical behaviors of the pristine Ce-MOF in aqueous electrolytes are investigated, suggesting that the pristine Ce-MOF is electrochemically active but possesses a limited charge-transport behavior. As a demonstration, all the Ce-MOF, CNT, and nanocomposites are used as active materials for application in aqueous-based supercapacitors. The capacitive performance of the CNT can be significantly boosted with the help of redox-active Ce-MOF-808 nanocrystals.

Selective Formation of Polyaniline Confined in the Nanopores of a Metal-Organic Framework for Supercapacitors.

In this study, a strategy that can result in the polyaniline (PANI) solely confined within the nanopores of a metal-organic framework (MOF) without forming obvious bulk PANI between MOF crystals is developed. A water-stable zirconium-based MOF, UiO-66-NH2 , is selected as the MOF material. The polymerization of aniline is initiated in the acidic suspension of UiO-66-NH2 nanocrystals in the presence of excess poly(sodium 4-styrenesulfonate) (PSS). Since the pore size of UiO-66-NH2 is too small to enable the insertion of the bulky PSS, the quick formation of pore-confined solid PANI and the slower formation of well dispersed PANI:PSS occur within the MOF crystals and in the bulk solution, respectively. By taking advantage of the resulting homogeneous PANI:PSS polymer solution, the bulk PANI:PSS can be removed from the PANI/UiO-66-NH2 solid by successive washing the sample with fresh acidic solutions through centrifugation. As this is the first time reporting the PANI solely confined in the pores of a MOF, as a demonstration, the obtained PANI/UiO-66-NH2 composite material is applied as the electrode material for supercapacitors. The PANI/UiO-66-NH2 thin films exhibit a pseudocapacitive electrochemical characteristic, and their resulting electrochemical activity and charge-storage capacities are remarkably higher than those of the bulk PANI thin films.