Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore ...the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (A
A
C
C
) relative to its two diploid progenitors, B. rapa (A
A
) and B. oleracea (C
C
), after approximately 7500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach.
The results showed that the 'transcriptomic shock' phenomenon was alleviated in natural B. napus after approximately 7500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (A
A
C
C
vs A
A
and A
A
C
C
vs C
C
), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27,609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48, 29.7 and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus.
In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7500 years of evolution and domestication and may enhance our understanding of allopolyploidy.
•A high-order time-delayed stochastic resonance tristable system is investigated.•The introduction of MFPT and the escape rate to describe the characteristics of escape.•The SR is researched by ...signal-to-noise ratio (SNR).•The effects for extracting weak fault signature signals are found.
A stochastic resonance (SR) tristable system based on a high-order time-delayed feedback is investigated and the feasibility of the system for weak fault signature extraction is discussed. The potential function, the mean first-passage time (MFPT) and the signal-to-noise ratio (SNR) are used to evaluate the model. Firstly, the potential function and stationary probability function (PDF) of the system are derived, and then the influence of the time delay parameters on the MFPT of the particles is analyzed. Secondly, the influences of time-delyed strength e and delyed length τ on the SR system from the perspective of the transition of the particles in the potential wells are discussed, and then the SNR and the effect of the parameters on the SNR are derived. In addition, the high-order time-delayed feedback tristable stochastic resonance (HTFTSR) system is used to deal with faulty bearing data and is compared with traditional tristable stochastic resonance (TSR). The result shows that the nonlinear system model can accurately identify the fault frequency and improve the energy of the characteristic signal under the appropriate system parameters.
Plant polyploidization increases the complexity of epigenomes and transcriptional regulation, resulting in genome evolution and enhanced adaptability. However, few studies have been conducted on the ...relationship between gene expression and epigenetic modification in different plant tissues after allopolyploidization. In this study, we studied gene expression and DNA methylation modification patterns in four tissues (stems, leaves, flowers and siliques) of Brassica napusand its diploid progenitors. On this basis, the alternative splicing patterns and cis-trans regulation patterns of four tissues in B. napus and its diploid progenitors were also analyzed. It can be seen that the number of alternative splicing occurs in the B. napus is higher than that in the diploid progenitors, and the IR type increases the most during allopolyploidy. In addition, we studied the fate changes of duplicated genes after allopolyploidization in B. napus. We found that the fate of most duplicated genes is conserved, but the number of neofunctionalization and specialization is also large. The genetic fate of B. napus was classified according to five replication types (WGD, PD, DSD, TD, TRD). This study also analyzed generational transmission analysis of expression and DNA methylation patterns. Our study provides a reference for the fate differentiation of duplicated genes during allopolyploidization.
WUSCHEL-related homeobox (WOX) genes encoding plant-specific homeobox (HB) transcription factors play important roles in the growth and development of plants. To date, WOX genes has been identified ...and analyzed in many polyploids (such as cotton and tobacco), but the evolutionary analysis of them during polyploidization is rare. With the completion of genome sequencing, allotetraploid Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are a good system for studying this question.
In this study, 52, 25 and 29 WOX genes were identified in allotetraploid B. napus (2n = 4x = 38, A
C
), the A
genome donor B. rapa (2n = 2x = 20, A
) and the C
genome donor B. oleracea (2n = 2x = 18, C
), respectively. All identified WOX genes in B. napus and its diploid progenitors were divided into three clades, and these genes were selected to perform gene structure and chromosome location analysis. The results showed that at least 70 and 67% of WOX genes maintained the same gene structure and relative position on chromosomes, respectively, indicating that WOX genes in B. napus were highly conserved at the DNA level during polyploidization. In addition, the analysis of duplicated genes and transposable elements (TEs) near WOX genes showed that whole-genome triplication (WGT) events, segmental duplication and abundant TEs played important roles in the expansion of the WOX gene family in B. napus. Moreover, the analysis of the expression profiles of WOX gene pairs with evolutionary relationships suggested that the WOX gene family may have changed at the transcriptional regulation level during polyploidization.
The results of this study increased our understanding of the WOX genes in B. napus and its diploid progenitors, providing a rich resource for further study of WOX genes in these species. In addition, the changes in WOX genes during the process of polyploidization were discussed from the aspects of gene number, gene structure, gene relative location and gene expression, which provides a reference for future polyploidization analysis.
The real-time monitoring on the risk status of the vehicle and its driver can provide the assistance for the early detection and blocking control of single-vehicle accidents. However, complex risk ...coupling relationship is one of the main features of single-vehicle accidents with high mortality rate. On the basis of investigating the coupling effect among multi-risk factors and establishing a safety management database throughout the life cycle of vehicles, single-vehicle driving risk network (SVDRN) with a three-level threshold was developed, and its topology features were analyzed to assessment the importance of nodes. To avoid the one-sidedness of single indicator, the multi-attribute comprehensive evaluation model was applied to measure the comprehensive effect of characteristic indicators for nodes importance. A algorithm for real-time monitoring of vehicle driving risk status was proposed to identify key risk chains. The result revealed that improper operation, speeding, loss of vehicle control and inefficient driver management were the sequence of top four risk factors in the comprehensive evaluation result of nodes importance (mean value = 0.185, SD = 0.119). There were minor differences of 0.017 in the node importance among environmental factors, among which non-standard road alignment had the larger value. The improper operation and non-standard road alignment were the highest combination correlation of factors affecting road safety, with the support of 51.81% and the confidence of 69.35%. This identification algorithm of key risk chains that combines node importance and its risk state threshold can effectively determine the high-frequency risk transmission paths and risk factors through multi-vehicle test, providing a basis for centralization management of transport enterprises.
A novel parameter estimation method is proposed for the permanent magnet synchronous generator (PMSG), which is implemented by an enhanced self‐learning particle swarm optimization algorithm with ...Levy flight (SLPSO), and the problem of lower parameter estimation precision of standard PSO is obviated. This method injects currents of different intensities into the d‐axis in a time‐sharing manner to solve the problem of equation under‐ranking, and the mathematical model for full‐rank parameter estimation is developed. The speed term of PSO is simplified to expedite the convergence of PSO, and a strategy with chaotic decline for the inertia weight of PSO is adopted to strengthen its ability to jump out of the local optimum. Moreover, the self‐learning dense fleeing strategy (SLDF) is proposed where particles perform diffusion learning based on population density information and Levy flight, the evolutionary unitary problem and human intervention in the evolutionary process is averted. Furthermore, the memory tempering annealing algorithm (MTA) and greedy algorithm (GA) is integrated into the algorithm, MTA can facilitate the exploration of potentially better regions, and GA for local optimization enhances the convergence speed and accuracy in late stage of the algorithm. Comparing the proposed method with several existing PSO algorithms through simulation and experiments, the experimental data show that the proposed method can effectively track variable parameters under different working conditions and has better robustness.
A novel parameter estimation method is proposed for the permanent magnet synchronous generator (PMSG), which is implemented by an enhanced self‐learning particle swarm optimization algorithm with Levy flight (SLPSO), and the problem of lower parameter estimation precision of standard PSO is obviated. This method injects currents of different intensities into the d‐axis in a time‐sharing manner to solve the problem of equation under‐ranking, and the mathematical model for full‐rank parameter estimation is developed. The speed term of PSO is simplified to expedite the convergence of PSO, and a strategy with Chaotic decline for the inertia weight of PSO is adopted to strengthen its ability to jump out of the local optimum.
Given the permeation of social media throughout society, rumors spread faster than ever before, which significantly complicates government responses to public health emergencies such as the COVID-19 ...pandemic.
We aimed to examine the characteristics and propagation of rumors during the early months of the COVID-19 pandemic in China and evaluated the effectiveness of health authorities' release of correction announcements.
We retrieved rumors widely circulating on social media in China during the early stages of the COVID-19 pandemic and assessed the effectiveness of official government clarifications and popular science articles refuting those rumors.
We show that the number of rumors related to the COVID-19 pandemic fluctuated widely in China between December 1, 2019 and April 15, 2020. Rumors mainly occurred in 3 provinces: Hubei, Zhejiang, and Guangxi. Personal social media accounts constituted the major source of media reports of the 4 most widely distributed rumors (the novel coronavirus can be prevented with "Shuanghuanglian": 7648/10,664, 71.7%; the novel coronavirus is the SARS coronavirus: 14,696/15,902, 92.4%; medical supplies intended for assisting Hubei were detained by the local government: 3911/3943, 99.2%; asymptomatically infected persons were regarded as diagnosed COVID-19 patients with symptoms in official counts: 322/323, 99.7%). The number of rumors circulating was positively associated with the severity of the COVID-19 epidemic (ρ=0.88, 95% CI 0.81-0.93). The release of correction articles was associated with a substantial decrease in the proportion of rumor reports compared to accurate reports. The proportions of negative sentiments appearing among comments by citizens in response to media articles disseminating rumors and disseminating correct information differ insignificantly (both correct reports: χ
=0.315, P=.58; both rumors: χ
=0.025, P=.88; first rumor and last correct report: χ
=1.287, P=.26; first correct report and last rumor: χ
=0.033, P=.86).
Our results highlight the importance and urgency of monitoring and correcting false or misleading reports on websites and personal social media accounts. The circulation of rumors can influence public health, and government bodies should establish guidelines to monitor and mitigate the negative impact of such rumors.
and its diploid progenitors (
and
) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of ...plants, and are crucial to plant growth, development, and stress response. In this study, the
gene family was comprehensively identified and analyzed, and 9, 9, and 24
genes were identified in
,
, and
, respectively. Phylogenetic analysis showed that all of the identified
genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified
genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of
genes is largely conserved during polyploidization. The promoters of the
genes in
contained more
-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus,
might have potential advantages in some biological aspects. In addition, the changes of
genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.
The fat mass and obesity-associated (FTO) gene plays a pivotal role in regulating body weight and fat mass; however, the underlying mechanisms are poorly understood. Here we show that primary ...adipocytes and mouse embryonic fibroblasts (MEFs) derived from FTO overexpression (FTO-4) mice exhibit increased potential for adipogenic differentiation, while MEFs derived from FTO knockout (FTO-KO) mice show reduced adipogenesis. As predicted from these findings, fat pads from FTO-4 mice fed a high-fat diet show more numerous adipocytes. FTO influences adipogenesis by regulating events early in adipogenesis, during the process of mitotic clonal expansion. The effect of FTO on adipogenesis appears to be mediated via enhanced expression of the pro-adipogenic short isoform of RUNX1T1, which enhanced adipocyte proliferation, and is increased in FTO-4 MEFs and reduced in FTO-KO MEFs. Our findings provide novel mechanistic insight into how upregulation of FTO leads to obesity.
Polyploidization promotes species formation and is widespread in angiosperms. Genome changes dramatically bring opportunities and challenges to plants after polyploidy. Methyl-CpG-Binding Domain ...(MBD) proteins can recognize and bind to methylation sites and they play an important role in the physiological process related to methylation in animals and plants. However, research on the influence of the allopolyploidization process on the MBD gene family is still lacking, so it is necessary to conduct a comprehensive analysis.
In this study, twenty-two, ten and eleven MBD genes were identified in the genome of allotetraploid B. napus and its diploid ancestors, B. rapa and B. oleracea, respectively. Based on the clades of the MBD gene in Arabidopsis, rice and maize, we divided the new phylogenetic tree into 8 clades. Among them, the true MBD genes in Brassica existed in only 5 clades. Clade IV and Clade VI were unique in term of MBD genes in dicotyledons. Ka/Ks calculations showed that MBD genes underwent purifying selection in Brassica and may retain genes through sequence or functional differentiation early in evolution. In the process of allopolyploidization, the number of MBD gene introns increased, and the protein motifs changed. The MBD proteins had their own special motifs in each clade, and the MBD domains were only conserved in their clades. At the same time, the MBD genes were expressed in flower, leaf, silique, and stem tissues, and the expression levels of the different genes were significantly different, while the tissue specificity was not obvious. The allopolyploidization process may increase the number of cis-acting elements and activate the transposable elements. During allopolyploidization, the expression pattern of the MBD gene changes, which may be regulated by cis-acting elements and transposable elements. The number imbalance of cis-acting elements and transposable elements in A
and C
subgenomes may also lead to biased A
subgenome expression of the MBD gene in B. napus.
In this study, by evaluating the number, structure, phylogeny and expression of the MBD gene in B. napus and its diploid ancestors, we increased the understanding of MBD genes in allopolyploids and provided a reference for future analysis of allopolyploidization.
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