Evolutionary Structure Research Articles

Multisample motif discovery and visualization for tandem repeats.

Tandem Repeats (TR) occupy a significant portion of the human genome and are the source of polymorphism due to variations in sizes and motif compositions. Some of these variations have been associated with various neuropathological disorders, highlighting the clinical importance of assessing the motif structure of TRs. Moreover, assessing the TR motif variation can offer valuable insights into evolutionary dynamics and population structure. Previously, characterizations of TRs have been limited by short-read sequencing technology, which lacks the ability to accurately capture the full TR sequences. As long-read sequencing becomes more accessible and can capture the full complexity of TRs, there is now also a need for tools to characterize and analyze TRs using long-read data across multiple samples. In this study, we present MotifScope, a novel algorithm for characterization and visualization of TRs based on a de novo k-mer approach for motif discovery. Comparative analysis against established tools reveals that MotifScope can identify a greater number of motifs and more accurately represent the underlying repeat sequence. Moreover, MotifScope has been specifically designed to enable motif composition comparisons across assemblies of different individuals, as well as across long-read sequencing reads within an individual, through combined motif discovery and sequence alignment. We showcase potential applications of MotifScope in diverse fields, including population genetics, clinical settings, and forensic analyses.

Two-dimensional Sc2O3 monolayer with tunable ultrawide bandgap for solar-blind ultraviolet photodetector

A novel 2D scandia (Sc2O3) monolayer was identified using an evolutionary algorithm-based crystal structure prediction method. The Sc2O3 monolayer exhibits a P3‾m1 symmetry and excellent energetic, thermal, dynamical, and mechanical stability, as well as good mechanical flexibility. The monolayer possesses an ultrawide indirect band gap of 6.246 eV. The monolayer is transparent in the visible light zone, while the large exciton effect leads to significant absorption in the solar-blind and vacuum ultraviolet regions. The band gap of this monolayer can be reduced monotonically by external biaxial tensile strain, resulting in the absorption spectrum covering the entire solar blind spectral region when the load reaches 5.0 %. Additionally, the monolayer has an ultra-high in-plane dielectric constant of approximately 50. The superior stability, flexibility, and strain-tunable electronic and optical properties, as well as the ultra-high dielectric constant, suggest its potential application in a solar-blind photodetector in harsh environments.

Forms of the Mother Right: Marxism's Matriarchal Origins from Friedrich Engels to Lu Märten

AbstractThe nineteenth‐century discovery of the matrilineal origins of society shattered assumptions about the necessity of the bourgeois family. For Marxists, ethnographic studies of the mother right provided an aesthetic form to reevaluate the “woman question” from a scientific perspective. Although Marx and Engels had long rejected the idea of the family in favor of “family forms,” Engels's adaptation of Morgan's Ancient Society (1877) in Der Ursprung der Familie, des Privateigentums und des Staats (1884) was canonized as the authoritative Marxist text on the subject. While the ethnographic form enabled the denaturalization of the family, its racialized and gendered temporality undercut socialist critiques of social forms. This article introduces Lu Märten's queer utopian response to the mother right, Geschichte der Frau vom Mutterrecht bis zur Gegenwart (1947), which dispenses with the evolutionary structure of the ethnographic study to offer a vision of polyamorous and androgynous forms in a classless society.

Transcriptome Wide Identification and Expression Analysis Revealed BhTALE Gene Family Regulates Wax Gourd (Benincasa hispida) Response to Low Calcium and Magnesium Stress

The three-amino-loop-extension (TALE) family involves key transcription factors vital for maintaining different aspects of growth including leaf, flower, and fruit development and responses to stressful stimulus. Thus far, a deep understanding of the TALE gene family in wax gourd subjected to low calcium and magnesium stress has been missing. Here, we isolated 24 BhTALE genes from a wax gourd genome database. Comprehensive bioinformatic analysis, including evolutionary tree, gene structures, conserved motifs, and chemical properties, provide structural and functional insights into the BhTALE gene family. Gene ontology (GO) analysis of TALE genes unveils their involvement in growth and stress responses. Promoter analysis indicates that hormones and stresses can influence the expression of BhTALE genes. Tissue-specific expression under low calcium and magnesium stress showed that BhTALE genes were more active in the leaves and roots. Notably, BhTALE7, BhTALE10, and BhTALE14 were expressed differentially in leaves under low calcium and magnesium applications. Similarly, the induced expression pattern of BhTALE4 was recorded in the roots under low calcium and magnesium applications. Our findings underscore the pivotal role of the BhTALE gene family in dealing with low calcium and magnesium stress in the wax gourd.

In silico Analysis and Characterization of the F5H Gene Family in Sorghum bicolor and Its Role in Lignin Production

Ferulate 5-hydroxylase (F5H), a cytochrome P450-dependent monooxygenase, catalyzes the hydroxylation of coniferaldehyde, a crucial step in the formation of syringyl lignin monomer (S). However, evolutionary divergence, expression patterns under abiotic stress conditions (ABA, PEG and NaOH) and lignin content-related features of the F5H gene family in Sorghum bicolor have not been explored. This study envisaged mining of Sorghum genomic data leading to the identification of 61 SbF5H genes. Bioinformatics analysis revealed the phylogenetic evolutionary relations, gene structures, conserved motifs, physicochemical properties, and promoter cis-acting elements related to these genes and their encoded proteins. Based on the gene structural and phylogenetic features, these 61 SbF5Hs were grouped into 4 subclasses. The in silico expression analysis revealed higher accumulation of SbF5H1 transcripts in embryo and in root under stress conditions. Similarly, Other SbF5H genes have shown expression in stem and root, thus indicating SbF5H genes involvement in Sorghum lignin biosynthesis. By exploring into the functional aspects of the F5H gene, our study sought to shed light on its significance in influencing not only the chemical makeup of lignin but also the resultant plant phenotypes. This insight into the molecular mechanisms governing lignin biosynthesis can have implications for bioenergy production and crop improvement.

Genome-wide identification of the OVATE family proteins and functional analysis of BhiOFP1, BhiOFP5, and BhiOFP18 during fruit development in wax gourd (Benincasa hispida)

OVATE family proteins (OFPs) are transcriptional regulators in plants. They have a common domain called the OVATE domain and control the development of leaves, fruits, and flowers in plants. Although the OFP gene family has been widely explored in the plant kingdom, the identification and characterization of this family have not yet been performed in wax gourd. In this study, we conducted a genome-wide investigation of the OFP gene family and identified 18 OFP (BhiOFP) genes in wax gourd. Next, we discovered their evolutionary relationships, conserved motifs, gene structures, cis-acting elements, and expression patterns. The BhiOFP genes were irregularly distributed on nine chromosomes, with only two BhiOFP genes containing introns. The BhiOFP gene promoters contained cis-acting elements in response to phytohormones and environmental signals. The majority of BhiOFP genes were derived from whole-genome duplication events. Expression analysis demonstrated that the BhiOFP genes showed disparate modes of expression and some of them were highly expressed in fruits. Overexpression of BhiOFP1, BhiOFP5, and BhiOFP18 in Arabidopsis resulted in dwarf plants, small rosette leaves, and shortened siliques, while the BhiOFP1 overexpression plants displayed a more severe phenotype. In summary, our study systematically analyzed the wax gourd OFP gene family, facilitated the functional research of BhiOFP1, BhiOFP5, and BhiOFP18, and offered a theoretical foundation for the improvement of wax gourd varieties with appropriate fruit length.

Chromosome-level genome assembly of Oriental chestnut gall wasp (Dryocosmus kuriphilus)

Dryocosmus kuriphilus, commonly known as the chestnut gall wasp, belongs to the family Cynipidae and is native to China. It is a highly invasive insect species causing serious damage to chestnut trees and has rapidly spread to various continents, including Europe, North America, and Oceania. The D. kuriphilus has become one of the important pests of chestnut plants in the world and is listed as a quarantine object by the European and Mediterranean Plant Protection Organization (EPPO). In this study, we used PacBio long reads, Illumina short reads, and Hi-C sequencing data to construct a chromosome-level assembly of the D. kuriphilus genome. The assembled genome includes 14,729 contigs with a total length of 2.28 Gb and a contig N50 of 0.8 Mb. With Hi-C technology, 2.17 Gb (95.02%) of contigs were anchored and oriented into the 10 pseudochromosomes with the scaffold N50 of 198.8 Mb and the scaffold N90 of 158.8 Mb. In total, 24,086 protein-coding genes were predicted in the assembled D. kuriphilus genome as the reference gene set. A total of 1.82 Gb repeats (occupying 79.7% of the genome), including 1.42 Gb of transposable elements and 0.40 Gb of tandem repeats, were identified in D. kuriphilus genome. In the evaluation of completeness, the BUSCO analysis determined a level of 98.1% completeness for the assembled genome sequences based on the Insecta database (OrthoDB version 10). The high-quality genome assembly of D. kuriphilus will not only provide a valuable reference for the study of its evolutionary history and genetic structure but also facilitate the research of host-pest interactions and invasiveness. Moreover, this genome assembly will promote in the development of effective management strategies to mitigate the economic and ecological impacts of this invasive pest on chestnut trees and ecosystems.

Prediction of novel layered indium halide superconductors

Abstract We design two new layered indium halide compounds LaOInF2 and LaOInCl2 by means of first-principles calculations and evolutionary crystal structure prediction. We find both compounds crystallize in a tetragonal structure with P4/nmm space group and have indirect band gaps of 2.58 eV and 3.21 eV, respectively. By substituting O with F, both of them become metallic and superconducting at low temperature. The F-doping leads to strong electron–phonon coupling in the low-energy acoustic phonon modes which is mainly responsible for the induced superconductivity. The total electron–phonon coupling strength are 1.86 and 1.48, while the superconducting transition temperature (T c) are about 7.2 K and 6.5 K with 10% and 5% F doping for LaOInF2 and LaOInCl2, respectively.

TaMYB-CC5 gene specifically expressed in root improve tolerance of phosphorus deficiency and drought stress in wheat

Phosphate deficiency and drought are significant environmental constraints that impact both the productivity and quality of wheat. The interaction between phosphorus and water facilitates their mutual absorption processes in plants. Under conditions of both phosphorus deficiency and drought stress, we observed a significant upregulation in the expression of wheat MYB-CC transcription factors through the transcriptome analysis. 52 TaMYB-CC genes in wheat were identified and analyzed their evolutionary relationships, structures, and expression patterns. The TaMYB-CC5 gene exhibited specific expression in roots and demonstrated significant upregulation under phosphorus deficiency and drought stress compared to other TaMYB-CC genes. The overexpression of TaMYB-CC5A in Arabidopsis resulted in a significant increase of root length under stress conditions, thereby enhancing tolerance to phosphate starvation and drought stress. The wheat lines with silenced TaMYB-CC5 genes exhibited reduced root length under stress conditions and increased sensitivity to phosphate deficiency and drought stress. In addition, silencing the TaMYB-CC5 genes resulted in altered phosphorus content in leaves but did not lead to a reduction in phosphorus content in roots. Enrichment analysis the co-expression genes of TaMYB-CC5 transcription factors, we found the zinc-induced facilitator-like (ZIFL) genes were prominent associated with TaMYB-CC5 gene. The TaZIFL1, TaZIFL2, and TaZIFL5 genes were verified specifically expressed in roots and regulated by TaMYB-CC5 transcript factor. Our study reveals the pivotal role of the TaMYB-CC5 gene in regulating TaZIFL genes, which is crucial for maintaining normal root growth under phosphorus deficiency and drought stress, thereby enhanced resistance to these abiotic stresses in wheat.

Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes.

Repeats can mediate rearrangements and recombination in plant mitochondrial genomes and plastid genomes. While repeat accumulations are linked to heightened evolutionary rates and complex structures in specific lineages, debates persist regarding the extent of their influence on sequence and structural evolution. In this study, 75 Plantago plastomes were analyzed to investigate the relationships between repeats, nucleotide substitution rates, and structural variations. Extensive repeat accumulations were associated with significant rearrangements and inversions in the large inverted repeats (IRs), suggesting that repeats contribute to rearrangement hotspots. Repeats caused infrequent recombination that potentially led to substoichiometric shifting, supported by long-read sequencing. Repeats were implicated in elevating evolutionary rates by facilitating localized hypermutation, likely through DNA damage and repair processes. This study also observed a decrease in nucleotide substitution rates for loci translocating into IRs, supporting the role of biased gene conversion in maintaining lower substitution rates. Combined with known parallel changes in mitogenomes, it is proposed that potential dysfunction in nuclear-encoded genes associated with DNA replication, recombination, and repair may drive the evolution of Plantago organellar genomes. These findings contribute to understanding how repeats impact organellar evolution and stability, particularly in rapidly evolving plant lineages.

Divergence of Phyllosphere Microbial Community Assemblies and Components of Volatile Organic Compounds between the Invasive Sphagneticola trilobata, the Native Sphagneticola calendulacea and Their Hybrids, and Its Implications for Invasiveness.

Closely-related plant groups with distinct microbiomes, chemistries and ecological characteristics represent tractable models to explore mechanisms shaping species spread, competitive dynamics and community assembly at the interface of native and introduced ranges. We investigated phyllosphere microbial communities, volatile organic compound (VOC) compositions, and potential interactions among introduced S. trilobata, native S. calendulacea and their hybrid in South China. S. trilobata exhibited higher α diversity but significantly different community composition compared to the native and hybrid groups. However, S. calendulacea and the hybrid shared certain microbial taxa, suggesting potential gene flow or co-existence. The potent antimicrobial VOC profile of S. trilobata, including unique compounds like p-cymene (13.33%), likely contributes to its invasion success. The hybrid's intermediate microbial and VOC profiles suggest possible consequences for species distribution, genetic exchange, and community assembly in heterogeneous environments. This hybrid deserves further study as both an opportunity for and threat to diversity maintenance. These differentiating yet connected plant groups provide insight into ecological and evolutionary dynamics shaping microbiome structure, species co-occurrence and competitive outcomes during biological exchange and habitat transformation. An interdisciplinary approach combining chemical and microbial ecology may reveal mechanisms underlying community stability and change, informing management of species spread in a globalized world.

Employing an optimisation algorithm to design an evolutionary topological structure for non-misbehaving nodes with optimal path selection

Employing an optimisation algorithm to design an evolutionary topological structure for non-misbehaving nodes with optimal path selection

A database of high-pressure crystal structures from hydrogen to lanthanum

This paper introduces the HEX (High-pressure Elemental Xstals) database, a complete database of the ground-state crystal structures of the first 57 elements of the periodic table, from H to La, at 0, 100, 200 and 300 GPa. HEX aims to provide a unified reference for high-pressure research, by compiling all available experimental information on elements at high pressure, and complementing it with the results of accurate evolutionary crystal structure prediction runs based on Density Functional Theory. Besides offering a much-needed reference, our work also serves as a benchmark of the accuracy of current ab-initio methods for crystal structure prediction. We find that, in 98% of the cases in which experimental information is available, ab-initio crystal structure prediction yields structures which either coincide or are degenerate in enthalpy to within 300 K with experimental ones. The main manuscript contains synthetic tables and figures, while the Crystallographic Information File (cif) for all structures can be downloaded from the related figshare online repository.

A novel variant c.902C>A (p. A301D) in KCNQ4 associated with non-syndromic deafness 2A in a Chinese family.

Deafness autosomal dominant 2A (DFNA2A) is related to non-syndromic genetic hearing impairment. The KCNQ4 (Potassium Voltage-Gated Channel Subfamily Q Member 4) can lead to DFNA2A. In this study, we report a case of autosomal dominant non-syndromic hearing loss with six family members as caused by a novel variant in the KCNQ4 gene. The whole-exome sequencing (WES) and pure tone audiometry were performed on the proband of the family. Sanger sequencing was conducted on family members to determine if the novel variant in the KCNQ4 gene was present. Evolutionary conservation analysis and computational tertiary structure protein prediction of the wild-type KCNQ4 protein and its variant were then performed. In addition, voltage-gated channel activity of the wild-type KCNQ4 protein and its variant were tested using whole-cell patch clamp. It was observed that the proband had inherited autosomal dominant, non-syndromic sensorineural hearing loss as a trait. A novel co-segregating heterozygous missense variant (c.902C>A, p.Ala301Asp) of the KCNQ4 gene was identified in the proband and other five affected family members. This variant was predicted to cause an alanine-to-aspartic acid substitution at position 301 in the KCNQ4 protein. The alanine at position 301 is well conserved across different species. Whole-cell patch clamp showed that there was a significant difference between the WT protein currents and the mutant protein currents in the voltage-gated channel activity. In the present study, performing WES in conjunction with Sanger sequencing enhanced the detection of a novel, potentially causative variant (c301 A>G; p.Ala301Asp) in exon 6 of the KCNQ4 gene. Therefore, our findings contributed to the mutation spectrum of the KCNQ4 gene and may be useful in the diagnosis and gene therapy of deafness autosomal dominant 2A.

An improved evolutionary structure optimization method considering stress minimization and smooth design

AbstractThe design of continuum structures often presents challenges related to stress concentration, which can cause significant structural damage. To address this issue, the current study presents a new stress minimization method that utilizes the Windowed Evolutionary Structural Optimization (WESO) framework. The method aims to improve algorithm stability by optimizing design variables with an intermediate density. The use of a P‐norm stress aggregation method improves the assessment of global stress levels and enhances computational efficiency. Furthermore, a stable element sensitivity formulation, derived from the adjoint sensitivity analysis of the global stress measure, effectively handles the nonlinear stress behavior. Mesh filtering techniques are utilized to convert sensitivity from elements to nodes, and the structural topological solution is represented using the level set function (LSF) based on element‐node sensitivity. This method addresses the singularity issue commonly found in density‐based optimization methods and facilitates the achievement of smooth topological solutions. Through 2D and 3D benchmark designs, the proposed method's feasibility, stability, and superiority are thoroughly demonstrated. A parametric study is conducted to identify the optimal parameter range for the algorithm, leading to the development of a rational method for parameter selection. The optimized topology, with its smooth boundaries, can guide the design of structures without the need for redesign or post‐processing, helping to drive innovation and development in engineering.

Electron-phonon driven superconductivity in the novel A15 phase of the Ti–Te system under pressure

We investigate the high-pressure phase diagram of Ti–Te system using first-principles calculations combined with evolutionary crystal structure prediction. Given the isostructural behavior of Se and Te at higher pressures, the same stoichiometric ratios as in the Ti–Se system were found in the Ti–Te system at high pressures. A novel A15 stable phase Ti3Te is predicted under pressure. Following this, its electronic, mechanical, vibrational, dynamical and superconducting properties at 0 GPa have been systematically scrutinized. The Ti-d orbitals occupy mainly at the Fermi level and Ti3Te exhibits intrinsic metallic property. Meanwhile, the electron-phonon coupling constant λ is 1.03, and the calculated superconducting transition temperature Tc (μ∗ = 0.10–0.15) is 14.2-11 K. Furthermore, we have studied the A15 structural candidates that can be formed by Ti and sulphur group elements under pressure. The mechanism of pressure-enhanced superconductivity present in these structures is also elucidated from a microscopic perspective.

Application of bi-directional evolutionary structural optimization to the design of an innovative pedestrian bridge

With rapid advances in design methods and structural analysis techniques, computational generative design strategies have been adopted more widely in the field of architecture and engineering. As a performance-based design technique to find out the most efficient structural form, topology optimization provides a powerful tool for designers to explore lightweight and elegant structures. Building on this background, this study proposes an innovative pedestrian bridge design, which covers the process from conceptualization to detailed design implementation. This pedestrian bridge, with a main span of 152 m, needs to meet some unique architectural requirements, while addressing multiple engineering challenges. Aiming to reduce the depth of the girder but still meeting the load-carrying capacity requirements, the superstructure of this bridge adopts a variable-depth spinal-shaped girder in the center of its deck, thus forming an elegant curving facade, from which one pathway cantilevers on either side. At one end of the bridge, given considerable elevation difference between the bridge deck and the ground, a two-level Fibonacci-type spiral-shaped bicycle ramp is provided. The superstructure is supported by a series of organic tree-shaped branching piers resulting from the topology optimization. The ingenious design for the elegant profile of the bicycle ramp generates an enjoyable and dynamic crossing experience, with scenic views in all directions. By virtue of technological innovation, the pedestrian bridge is expected to create an iconic, cost-effective, and low-maintenance solution. A brief overview of the theoretical background of the bi-directional evolutionary structure optimization (BESO) and the multi-material BESO approach is also offered in this paper, while the construction requirements and challenges, conceptual development process, form-finding strategy, detailed design, and construction method of the bridge are presented.

Seeing what you believe: recognition memory for evolutionary tree structure is affected by students’ misconceptions

ABSTRACT Peoples’ recognition memory for pictorial stimuli is extremely good. Even complex scientific visualisations are recognised with a high degree of accuracy. The present research examined recognition memory for the branching structure of evolutionary trees. This is an educationally consequential topic due to the potential for contamination from students’ misconceptions. The authors created six pairs of scientifically accurate and structurally identical evolutionary trees that differed in whether they included a taxon that cued a misconception in memory. As predicted, Experiment 1 found that (a) college students (N = 90) had better memory for each of the six tree structures when a neutral taxon (M = 0.73) rather than a misconception-cuing taxon (M = 0.64) was included in the tree, and (b) recognition memory was significantly above chance for both sets of trees. Experiment 2 ruled out an alternative hypothesis based on the possibility that 8–12 sec was not enough time for students to encode the relationships depicted in the trees. The authors consider implications of these results for using evolutionary trees to better communicate scientific information. This is important because these trees provide information that is relevant for everyday life.

Remarkable Optoelectronic Characteristics of Synthesizable Square‐Octagon Haeckelite Structures: Machine Learning Materials Discovery

AbstractThe research explores new compounds with structures similar to square‐octagonal beryllium oxide, commonly known as Haeckelites. The goal is to identify semiconducting variations compounds that can be synthesized and show promising potential in optoelectronic devices. Start with 1083 binary Haeckelite structures, and to test the synthesis potential of these materials quickly, develop new descriptors and use machine learning techniques. As a result, it identifies a subset of 350 materials with suitable properties in terms of phase stability and electronic perspective. These materials are further investigated to analyze their electronic structure and phase stability, which are determined through density functional theory calculations. The phase stabilities of the predicted semiconducting Haeckelites are also compared to other binary compounds using an evolutionary structure search algorithm. The comprehensive methodology also includes examining the dynamic stabilities through phonon calculations and mechanical properties through elastic constant calculations. Eventually, 13 new Haeckelite compounds are discovered, demonstrating exceptional stability and performance in electronic tests. Among these compounds, eight have shown remarkable absorption coefficients and are considered promising candidates with high reflectivity. Additionally, they have exhibited high electron mobility. These findings strongly suggest the potential of these compounds for synthesis and their application in optoelectronic devices.

Multi-group symbiotic evolutionary mechanisms of a digital innovation ecosystem: Numerical simulation and case study.

In the digital innovation ecosystem, the symbiosis mode formed between ecosystem members not only relates to their survival and development but also affects the ecosystem's symbiosis evolution mechanism. Based on symbiosis theory, this study first explores the evolutionary equilibrium strategy and its stability for three types of populations-core enterprises, digital platforms, and university research institutes-and then uses numerical simulation and a case study to explore the symbiotic evolution mechanism of the digital innovation ecosystem. The results show that: First, the digital innovation ecosystem is a complex adaptive system in which the three types of populations form different symbiotic relationships under different symbiotic modes and conduct symbiotic activities, such as value co-creation, to characterize the unique symbiotic evolutionary structure. Second, in this ecosystem, the symbiotic relationship formed by the combined values of different symbiotic coefficients between populations determines the outcome of symbiotic evolution. Third, the ideal direction of the evolution of the digital innovation ecosystem is a mutually beneficial symbiotic relationship. Thus, the symbiotic relationship between populations should be transformed into a mutually beneficial symbiotic relationships as much as possible. This study makes theoretical contributions by shedding light on the symbiotic evolution mechanism of the digital innovation ecosystem. It also offers countermeasures for the digital innovation cooperation of various stakeholders in China's digital innovation ecosystem.