Search Results (235)

Peanut (Arachis hypogaea L.) is a globally important oilseed cash crop, yet its limited genetic diversity and unique reproductive biology present persistent challenges for conventional crossbreeding. Traditional breeding approaches are often time-consuming and inadequate, mitigating the pace of cultivar development. Essential for double fertilization and programmed cell death (PCD), DUF679 membrane proteins (DMPs) represent a membrane protein family unique to plants. In the present study, a comprehensive analysis of the DMP gene family in peanuts was conducted, which included the identification of 21 family members. Based on phylogenetic analysis, these genes were segregated into five distinct clades (I–V), with AhDMP8A, AhDMP8B, AhDMP9A, and AhDMP9B in clade IV exhibiting high homology with known haploid induction genes. These four candidates also displayed significantly elevated expression in floral tissues compared to other organs, supporting their candidacy for haploid induction in peanuts. Subcellular localization prediction, confirmed through co-localization assays, demonstrated that AhDMPs primarily localize to the plasma membrane, consistent with their proposed roles in the reproductive signaling process. Furthermore, chromosomal mapping and synteny analyses revealed that the expansion of the AhDMP gene family is largely driven by whole-genome duplication (WGD) and segmental duplication events, reflecting the evolutionary dynamics of the tetraploid peanut genome. Collectively, these findings establish a foundational understanding of the AhDMP gene family and highlight promising targets for future applications in haploid induction-based breeding strategies in peanuts. Full article

For systems such as the van der Pol and van der Pol–Duffing oscillators, the study of their oscillation is currently a very active area of research. Many authors have used the bifurcation method to try to determine oscillatory behavior. But when the system involves n separate delays, the equations for bifurcation become quite complex and difficult to deal with. In this paper, the existence of periodic oscillatory behavior was studied for a system consisting of n coupled equations with multiple delays. The method begins by rewriting the second-order system of differential equations as a larger first-order system. Then, the nonlinear system of first-order equations is linearized by disregarding higher-degree terms that are locally small. The instability of the trivial solution to the linearized equations implies the instability of the nonlinear equations. Periodic behavior often occurs when the system is unstable and bounded, so this paper also studied the boundedness here. It follows from previous work on the subject that the conditions here did result in periodic oscillatory behavior, and this is illustrated in the graphs of computer simulations. Full article

The Duffing–van der Pol oscillator is a very prominent and interesting standard model. There is a substantial body of varied literature on this topic. In this article, we propose a new class of oscillators by adding new factors to its dynamics. Investigations in light of Melnikov’s approach are considered. Several simulations are composed. A few specialized modules for testing the dynamics of the hypothetical oscillator under consideration are also given. This will be an essential component of a much broader Web-based scientific computing application that is planned. Possible control over oscillations: approximation with restrictions is also discussed; some probabilistic constructions are also presented. Full article

Background/Objectives: The aetiology of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), a chronic and severe debilitating disease with a complex phenotype, remains elusive. Associations with infectious diseases and autoimmune and neuropsychiatric disorders have been observed, without the identification of mechanisms. Previous studies suggest that genetic predisposition plays a role, but results are difficult to replicate, with Genome-Wide Association Studies of ME/CFS being challenging due to the relative rareness and heterogeneity of the disorder. Methods: We studied a well-defined Australian patient cohort diagnosed via the International Consensus Criteria, recruited by a specialist ME/CFS clinic. The whole-exome sequences of 77 patients were contrasted against genome variation in the 1000 Genome Project’s genome-matched population. Results: Significant associations with ME/CFS were harboured in genes that belong to the Neuroblastoma Breakpoint Family encoding Olduvai (DUF1220) domains, namely NBPF1 (rs3897177, p-value = 3.15 × 10⁻⁸), NBPF10 (rs1553120233, p-value = 9.262 × 10⁻¹³), and NBPF16 (rs200632836, p-value = 1.04 × 10⁻⁶). Other significantly associated variants were detected in the ATR, RSPH10B, ADGRE5-CD97, and NTRK2 genes, among others. Replication of these results was attempted via a GWAS on raw data from a US cohort, which confirmed shared significant associations with variation identified in the PTPRD, CSMD3, RAPGEF5, DCC, ALDH18A1, GALNT16, UNC79, and NCOA3 genes. Conclusions: These genes are involved in cortical neurogenesis, brain evolution, and neuroblastoma, and have been implicated by several studies in schizophrenia and autism. The sharing of these associations by the two cohorts supports their validity and grants the necessity of future studies to evaluate the implications for ME/CFS aetiology. Full article

This paper presents the derivation of an exact solution for a damped nonlinear oscillator of arbitrary order (both integer and non-integer). A coefficient relationship was defined under which such a solution exists. The analytical procedure was developed based on the application of the Ateb (inverse beta) function. It has been shown that an exact solution exists for a specific relationship between the damping coefficient and the coefficient of the linear elastic term, and that this relationship depends on the order of nonlinearity. The exact amplitude of vibration was found to be a time-decreasing function, depending on the initial amplitude, damping coefficient, and the order of nonlinearity. The period of vibration was also shown to depend not only on the amplitude but also on both the nonlinearity coefficient and its order. For cases where the damping coefficient of the exact oscillator is slightly perturbed, an approximate solution based on the exact one was proposed. Three illustrative examples of oscillators with different orders of nonlinearity were considered: a nearly linear oscillator, a Duffing oscillator, and one with strong nonlinearity. For all cases, the high accuracy of the asymptotic solution was confirmed. Since no exact analytic solution exists for a purely nonlinear damped oscillator, an approximate solution was constructed using the solution of the corresponding undamped oscillator with a time-varying amplitude and phase. In the case of a purely cubic damped oscillator, the approximate solution was compared with numerical results, and good agreement was demonstrated. Full article

The PADRE (Pathogen and abiotic stress response, cadmium tolerance, disordered region-containing) family of genes, which contains the structural DUF4228 domain of unknown function (DUF), has been reported to be associated with plant responses to abiotic stresses. However, the specific functions of this family in the salt stress response remain unknown. AtPADRE13 is induced by salt stress and ABA (abscisic acid). After the overexpression of AtPADRE13 in Arabidopsis, seeds were found to be insensitive to ABA treatment. After salt treatment, the overexpression lines presented a significantly lower survival rate, increased MDA (Malondialdehyde) content, and reduced antioxidant enzyme activities compared with the wild-type, and were more sensitive to salt stress. Transcriptome data analysis further revealed that AtPADRE13 overexpression resulted in different degrees of down-regulation for a series of positive regulators related to ABA catabolism, transport, and their mediated plant responses to salt stress. In addition, the expression of genes related to ROS (reactive oxygen species) scavenging was down-regulated. In conclusion, AtPADRE13 plays a negative regulatory role in the response to salt stress in Arabidopsis. Full article

‘Candidatus Phytoplasma mali’ is associated with apple proliferation, a devastating disease in fruit production. Using genome analysis, a gene encoding a hemolysin-like protein was identified. It was postulated that this protein could be an effector. However, the function of this protein is unknown. It is shown that the hemolysin-like protein binds to a GTP binding protein, Toc33, of Arabidopsis thaliana in yeast two-hybrid analysis and that the Toc33-binding domain is located in the C-terminus of the domain of unknown function (DUF21) of the protein. The biochemical studies reveal that the protein can hydrolyze phosphate of purine and pyrimidine nucleotides. Transgenic Nicotiana benthamiana plants expressing the protein show no discernible change in phenotype. Phytoplasma have a much-reduced genome, lacking important genes for catabolic pathways or nucleotide production; therefore, the hemolysin-like protein plays a role in the uptake of plant nucleotides from their host and hydrolyzes these nucleotides for energy and their own biosynthesis. Full article

In this study, we propose a new nonlinear polarization model that modifies the polarization equation to account for the material’s nonlinear response. Specifically, the nonlinear restoring force in our model is reformulated as an electric field-dependent function, derived from the nonlinear Lorentz model. Additionally, we perform a comparative analysis of the Kerr model, the Duffing model, the nonlinear Lorentz model, and our modified nonlinear Lorentz model (MNL) by solving Maxwell’s equations using the finite-difference time-domain (FDTD) method. This research focuses on the third-order nonlinearity of these models under varying light intensities and different ratios of resonant frequency to carrier frequency. First, in the example we studied, our results show that the MNL model produces results closer to the Kerr model when the light intensity is significantly high. Second, the comparison under different resonant frequencies reveals that all models converge to the Kerr model when the carrier frequency is much lower than the resonant frequency. However, when the carrier frequency significantly exceeds the resonant frequency, the differences between the Kerr model and the other models become more noticeable. The third-order nonlinearity of our MNL model aligns more closely with the Kerr model than the nonlinear Lorentz and Duffing models do when the ratio of resonant frequency to carrier frequency is between 1 and 2. Full article

The 3-dimensional modified van der Pol–Duffing oscillator has been studied by several authors. We complete its study, first characterizing its zero-Hopf equilibria and then its zero-Hopf bifurcations—i.e., we provide sufficient conditions for the existence of three, two or one periodic solutions, bifurcating from the zero-Hopf equilibrium localized at the origin of coordinates. Recall that an equilibrium point of a 3-dimensional differential system whose eigenvalues are zero and a pair of purely imaginary eigenvalues is a zero-Hopf equilibrium. Finally, we determine the dynamics of this system near infinity, i.e., we control the orbits that escape to or come from the infinity. Full article

Two nonlinear Duffing equations are numerically treated in this article. The nonlinear fractional-order Duffing equations and the second-order nonlinear Duffing equations are handled. Based on the collocation technique, we provide two numerical algorithms. To achieve this goal, a new family of basis functions is built by combining the sets of Fibonacci and Lucas polynomials. Several new formulae for these polynomials are developed. The operational matrices of integer and fractional derivatives of these polynomials, as well as some new theoretical results of these polynomials, are presented and used in conjunction with the collocation method to convert nonlinear Duffing equations into algebraic systems of equations by forcing the equation to hold at certain collocation points. To numerically handle the resultant nonlinear systems, one can use symbolic algebra solvers or Newton’s approach. Some particular inequalities are proved to investigate the convergence analysis. Some numerical examples show that our suggested strategy is effective and accurate. The numerical results demonstrate that the suggested collocation approach yields accurate solutions by utilizing Fibonacci–Lucas polynomials as basis functions. Full article

Plant small peptides are critical regulators of various biological processes, including development and stress responses. Polypeptides within the DUF3774 family, known as wound-induced polypeptides (WIPs), have been identified as key players in pattern-triggered immunity (PTI) and defense mechanisms in Arabidopsis. In this study, the genome-wide identification of WIP genes in Glycine max was performed, followed by gene structure correction and validation using second-generation and full-length RNA sequencing data. A total of 31 GmWIP genes were identified and validated, mapped to chromosomes Gm06, Gm12, Gm13, and Gm06_scaffold_301. Phylogenetic analysis grouped these genes into five distinct clusters, with tandem duplication emerging as the primary mechanism for their expansion in the soybean genome. qRT-PCR analysis revealed dynamic and significant changes in GmWIP expression during soybean cyst nematode (SCN) infection in a susceptible soybean cultivar. Remarkably, 90% of the GmWIP genes were downregulated at the early stage of SCN infection (1 dpi), and further corroborated by the pGmWIPs::GUS reporter system. These findings suggest that GmWIP genes may act as regulators in the defense responses of susceptible soybean cultivars, providing a foundation for future functional studies. Full article

The Melnikov method is applied to a class of generalized Ziegler pendulums. We find an analytical form for the separatrix of the system in terms of Jacobian elliptic integrals, holding for a large class of initial conditions and parameters. By working in Duffing approximation, we apply the Melnikov method to the original Ziegler system, showing that the first non-vanishing Melnikov integral appears in the second order. An explicit expression for the Melnikov integral is derived in the presence of a time-periodic external force and for a suitable choice of the parameters, as well as in the presence of a dissipative term acting on the lower rod of the pendulum. These results allow us to define fundamental relationships between the Melnikov integral and a proper control parameter that distinguishes between regular and chaotic orbits for the original dynamical system. Finally, in the appendix, we present proof of a conjecture concerning the non-validity of Devaney’s chaoticity definition for a discrete map associated with the system. Full article

Background/Objectives: The MAST kinases are ancient AGC kinases associated with many human diseases, such as cancer, diabetes, and neurodevelopmental disorders. We set out to describe the origins and diversification of MAST kinases from a structural and bioinformatic perspective to inform future research directions. Methods: We investigated MAST-lineage kinases using database and sequence analysis. We also estimate the functional consequences of disease point mutations on protein stability by integrating predictive algorithms and AlphaFold. Results: Higher-order organisms often have multiple MASTs and a single MASTL kinase. MAST proteins conserve an AGC kinase domain, a domain of unknown function 1908 (DUF), and a PDZ binding domain. D. discoideum contains MAST kinase-like proteins that exhibit a characteristic insertion within the T-loop but do not conserve DUF or PDZ domains. While the DUF domain is conserved in plants, the PDZ domain is not. The four mammalian MASTs demonstrate tissue expression heterogeneity by mRNA and protein. MAST1-4 are likely regulated by 14-3-3 proteins based on interactome data and in silico predictions. Comparative ΔΔG estimation identified that MAST1-L232P and G522E mutations are likely destabilizing. Conclusions: We conclude that MAST and MASTL kinases diverged from the primordial MAST, which likely operated in both biological niches. The number of MAST paralogs then expanded to the heterogeneous subfamily seen in mammals that are all likely regulated by 14-3-3 protein interaction. The reported pathogenic mutations in MASTs primarily represent alterations to post-translational modification topology in the DUF and kinase domains. Our report outlines a computational basis for future work in MAST kinase regulation and drug discovery. Full article

Proteins of the PF10950 family feature the DUF2775 domain of unknown function. The most studied are specific tissue (ST) proteins with tandem repeats, which are putative precursors of cyclopeptide alkaloids. Here, we study uncharacterised short ST (SST) proteins with the DUFF2775 domain by analysing 194 sequences from 120 species of 39 taxonomic families in silico. SST proteins have a signal peptide and their size and several other characteristics depend on their individual taxonomic family. Sequence analyses revealed that SST proteins contain two well-conserved regions, one resembling the ST repeat, which could constitute the core of cyclopeptide alkaloids. We studied the unique SST1 gene of Arabidopsis thaliana, which is adjacent to and co-expressed with a gene encoding a protein with a BURP domain, associated with cyclopeptide production. The empirical analysis indicated that the SST1 promoter is mainly activated in the roots, where most of the transcripts accumulate, and that the SST1 protein accumulates in the root vascular cambium. At the cellular level, SST fused to GFP appears in vesicles that co-localise with the endoplasmic reticulum and the vacuole. Thus, SSTs are a new type of PF10950 protein found in core eudicots with two conserved regions that could be involved in root biology. Full article

The literature devoted to the issue of a forced modified Van der Pol–Duffing oscillator with asymmetric potential is a major and varied way to represent nonlinear dissipative chemical dynamics. It is known that this model is based on the real reaction–kinetic scheme. In this paper, we suggest a novel class of oscillators that are appealing to users due to their numerous free parameters and asymmetric potential. The rationale for this is because an expanded model is put out that enables the investigation of both classical and more recent models that have been reported in the literature at a “higher energy level”. We present a few specific modules for examining these oscillators’ behavior. A much broader Web-based application for scientific computing will incorporate this as a key component. Probabilistic construction to offer possible control over the oscillations is also considered. Full article