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26 pages, 2568 KB  
Article
Material Degradation Assessment in Hydrogenation Reactors: Multi-Mechanism Coupled Methodology and Application
by Juanbo Liu, Hao Zhou, Demin Zhou, Dong Jin, Sheng Chen and Zhiyuan Han
Processes 2026, 14(17), 2684; https://doi.org/10.3390/pr14172684 - 22 Aug 2026
Abstract
Hydrogenation reactors are critical equipment in the petrochemical industry, yet their material degradation is governed by coupled multi-mechanism damage. Current assessment practices largely neglect this complexity, remaining single-factor oriented and overlooking synergistic interactions and temporal evolution. This paper proposes a regionally differentiated, multi-level [...] Read more.
Hydrogenation reactors are critical equipment in the petrochemical industry, yet their material degradation is governed by coupled multi-mechanism damage. Current assessment practices largely neglect this complexity, remaining single-factor oriented and overlooking synergistic interactions and temporal evolution. This paper proposes a regionally differentiated, multi-level framework integrating 5 primary and 17 secondary indicators with a hybrid AHP-EWM weighting strategy that synthesizes expert knowledge and measured data. A multi-factor coupling correction coefficient is introduced to provide a preliminary estimate of the synergistic acceleration effect among damage mechanisms, while a GM(1,1) gray model enables dynamic trend prediction. Applied to a 25-year 2.25Cr-1Mo steel reactor, the method produces regional degradation values of 0.378, 0.607, and 0.533 for the base metal, welds, and cladding layer, respectively, with an overall baseline of 0.453 rising by 11% to 0.503 after coupling correction. Compared with exponential regression, ARIMA, and BP neural networks, GM(1,1) is selected for its balanced performance in small-sample fitting, extrapolation stability, and physical interpretability. Sensitivity analysis confirms stable degradation grading even with ±50% coupling coefficient variations. The proposed approach mitigates the underestimation inherent in conventional single-mechanism assessments and offers a quantitative tool for full-lifecycle risk management and predictive maintenance of hydrogenation reactors. Full article
(This article belongs to the Topic Green and Sustainable Chemical Products and Processes)
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24 pages, 10840 KB  
Article
Orbital Impulsive Pursuit–Evasion Game in the Cislunar Space
by Xujing Zhang, Shaofeng Li and Youliang Wang
Aerospace 2026, 13(8), 750; https://doi.org/10.3390/aerospace13080750 - 21 Aug 2026
Viewed by 152
Abstract
A pursuer and an evader can exploit low-energy, non-Keplerian trajectories in cislunar space, making it difficult to obtain the saddle point for impulsive orbital pursuit–evasion games (OPEG). To address this problem, this paper first establishes a zero-sum differential game model based on the [...] Read more.
A pursuer and an evader can exploit low-energy, non-Keplerian trajectories in cislunar space, making it difficult to obtain the saddle point for impulsive orbital pursuit–evasion games (OPEG). To address this problem, this paper first establishes a zero-sum differential game model based on the circular restricted three-body problem (CR3BP), where the terminal interception time is taken as the performance objective. The necessary optimality conditions for impulsive maneuvers are then derived using Pontryagin’s Maximum Principle (PMP), which transforms the optimal control problem into multipoint boundary value problems (MPBVPs). Subsequently, to overcome the high sensitivity of the MPBVPs to initial costate vectors in shooting methods, a two-layer hybrid initial-guess strategy combining a genetic algorithm with a time-domain coarse-grid search method is proposed for the single-impulse case. Furthermore, a receding-horizon strategy is introduced to generate the initial impulse sequence guess stage by stage for multiple-impulse cases. Finally, numerical simulations demonstrate that the proposed initial-guess strategy can effectively obtain the Stackelberg equilibrium solution for representative cislunar scenarios, including distant retrograde orbits (DROs) and Halo orbits. Meanwhile, the effects of observation delay and three-dimensional orbital characteristics on the game outcomes are also discussed based on dynamic game theory. Full article
(This article belongs to the Special Issue Spacecraft Trajectory Design)
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2 pages, 152 KB  
Abstract
Population Structure in Squalius laietanus: Evidence from mtDNA Control Region Diversity
by Nuria Perez-Bielsa, Lilith Weimer, Helena Mas, Sandra Heras, Jose-Luis Garcia-Marin and Alba Abras
Proceedings 2026, 146(1), 53; https://doi.org/10.3390/proceedings2026146053 - 17 Jun 2026
Viewed by 293
Abstract
Introduction: The Catalan chub (Squalius laietanus) is a freshwater cyprinid endemic to Catalonia, from the lower course of the Ebro River to the Tech, Tet, Agly, and Massane rivers in France. Classified as Vulnerable in the IUCN Red List (2024), its [...] Read more.
Introduction: The Catalan chub (Squalius laietanus) is a freshwater cyprinid endemic to Catalonia, from the lower course of the Ebro River to the Tech, Tet, Agly, and Massane rivers in France. Classified as Vulnerable in the IUCN Red List (2024), its populations face significant threats due to anthropogenic pressures and the potential hybridization with the European chub (Squalius cephalus). Objective: This study aimed to characterize the genetic variation of the mitochondrial control region (CR) of S. laietanus across the main Catalan river basins to determine the population genetic structure of this species in the core of its distribution range. Methodology: A 789 bp fragment of the CR was sequenced in 334 chubs from 24 sampling sites collected by electrofishing between 2021 and 2025. The S. laietanus specific matrilineage of all these specimens had been previously detected by sequencing the Cytochrome c oxidase subunit I (COI) but this marker did not detect clear genetic structuring among basins. Results: In contrast to the low diversity within and among locations reported by COI, the CR showed a population structure distinguishing between northern (Muga, Fluvià, Daró, Ter, and Tordera rivers) and southern basins (Besòs, Llobregat, Gaià, Francolí, and Ebro rivers). In the southern rivers, a single haplotype, (H1), was present. This haplotype declined in abundance towards the north, being replaced with H2. In the Muga River, native Catalan chub populations showed the fixed H3 haplotype, suggesting strong isolation, while populations from the Daró River contained a private haplotype (H4). In contrast, the presence of a common and single haplotype in southern basins possibly resulted from genetic drift under strong summer droughts. Conclusions: Overall, these results reveal population structuring in S. laietanus and highlight the importance of considering regional differentiation in conservation and management strategies. Full article
(This article belongs to the Proceedings of The XI Iberian Congress of Ichthyology)
15 pages, 1014 KB  
Article
Acute Creatine Ingestion Before Resistance Training Enhances Strength Performance More than Ingestion During or After Training: A Randomized Crossover Pilot Trial
by Khouloud Ben Maaoui, Slaheddine Delleli, Arwa Jebabli, Nourhène Mahdi, Juan Del Coso, Hamdi Chtourou, Luca Paolo Ardigò and Ibrahim Ouergui
Nutrients 2026, 18(11), 1789; https://doi.org/10.3390/nu18111789 - 1 Jun 2026
Viewed by 5739
Abstract
Background/Objectives: Although creatine (Cr) supplementation is well established for enhancing strength exercise adaptations, limited evidence exists regarding whether the timing of a single Cr dose relative to exercise acutely influences performance and related physiological and perceptual responses. This study examined whether the [...] Read more.
Background/Objectives: Although creatine (Cr) supplementation is well established for enhancing strength exercise adaptations, limited evidence exists regarding whether the timing of a single Cr dose relative to exercise acutely influences performance and related physiological and perceptual responses. This study examined whether the timing of a single dose of Cr ingestion relative to a strength exercise session influences acute strength and power performance, cognitive function, perceptual responses, and selected blood biomarkers in physically active men. Methods: In a randomized, placebo-controlled crossover design, 11 physically active men (26.09 ± 4.39 years) completed five experimental conditions: Cr ingested before exercise (CrB), during exercise (CrD), and after exercise (CrF), placebo (PL), and a no-supplement control. Participants ingested 0.1 g·kg−1 body mass of monohydrate Cr or placebo. Each condition included a standardized strength training session, where bench press (BP) and back squat (BSQ) performance was assessed as the total external load lifted (kg) across six sets performed at 80% of 1-RM for each exercise. Countermovement jump (CMJ) performance, Profile of Mood States (POMS), cognitive performance (digit cancelation test), perceived exertion (RPE), perceived recovery scale (PRS), Delayed-Onset Muscle Soreness (DOMS), and blood markers of muscle damage and renal function were assessed after the resistance training session. Data were analyzed using repeated-measures ANOVA or non-parametric equivalents, with post hoc comparisons adjusted for multiple testing. Results: There was a significant main effect of condition for both BP (F = 4.91, ηp2 = 0.33, p = 0.035) and BSQ performance (F = 33.22, ηp2 = 0.77, p < 0.001), with greater performance under the CrB condition compared with PL and control (p < 0.05). A significant effect of condition was also observed for creatine kinase (χ2 (4) = 12.22, p = 0.016) and creatinine concentrations (χ2 (4) = 17.75, p = 0.001). Blood creatine kinase concentrations were greater under CrF conditions than control (p = 0.013) and PL (p = 0.041). Moreover, creatinine concentration was lower under the CrB condition compared to CrD (p = 0.033), CrF (p = 0.003), and the control (p = 0.021). No differences were observed for CMJ performance, cognitive performance, POMS, RPE, PRS, DOMS, or the remaining biochemical markers across treatments. Conclusions: Pre-exercise creatine ingestion (without loading phase) was associated with greater acute strength performance compared with other timing conditions. However, the findings are exploratory and have to be confirmed with a higher sample size and robust placebo/control structures. Full article
(This article belongs to the Special Issue Nutrition Strategy and Resistance Training)
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34 pages, 6742 KB  
Article
Multi-Objective Optimization of U-Drill Chip-Groove Structural Parameters Based on GA–BP and NSGA-II Algorithms
by Zhipeng Jiang, Yao Liang, Xiangwei Liu, Xianli Liu, Guohua Zheng and Yuxin Jia
Coatings 2026, 16(3), 346; https://doi.org/10.3390/coatings16030346 - 10 Mar 2026
Cited by 3 | Viewed by 723
Abstract
To address the poor cutting stability and deterioration of hole quality caused by the inherent trade-off between chip evacuation performance and drill-body stiffness in U-drilling, a multi-objective optimization framework was established. The design variables were the core thicknesses L1 and L2 [...] Read more.
To address the poor cutting stability and deterioration of hole quality caused by the inherent trade-off between chip evacuation performance and drill-body stiffness in U-drilling, a multi-objective optimization framework was established. The design variables were the core thicknesses L1 and L2 of the inner and outer chip flutes, the inner and outer offset angles θ1 and θ2, and the inner and outer helix angles β1 and β2. The objectives were to maximize the chip evacuation force and minimize the drill-body strain (which serves as an equivalent indicator of maximizing drill-body stiffness). The chip evacuation force was rapidly evaluated using a mechanistic chip evacuation force model derived from mechanism-based analysis. The drill-body strain was efficiently predicted using a GA–BP neural-network surrogate model. An NSGA-II algorithm combined with the entropy-weighted TOPSIS method was employed to solve the optimization problem, yielding the optimal parameter combination for the U-drill chip-flute geometry. The results show that drilling experiments on 42CrMo under the optimal structural parameter combination reduced the cutting forces in the x, y, and z directions by approximately 11.2%, 13.1%, and 11.8%, respectively. The root-mean-square acceleration in the x and y-directions decreased by about 17.3% and 22.9%, respectively. These improvements effectively enhanced the hole-wall surface roughness and hole diameter accuracy, and further improved chip evacuation smoothness and cutting stability of the U-drill. Full article
(This article belongs to the Special Issue Cutting Performance of Coated Tools)
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15 pages, 710 KB  
Article
An Assessment of the Effect of HIV and ART on Cardiovascular Risk Factors to Predict Retinal Microvascular Impairment in Pregnant Women: A Pilot Study in a South African Population
by Edna N. Matjuda, Benedicta N. Nkeh-Chungag, Godwill A. Engwa, Constance R. Sewani-Rusike, Nontsikelelo C. Gubu-Ntaba, Charles B. Businge, Adam Saloň, Patrick De Boever and Nandu Goswami
J. Vasc. Dis. 2026, 5(2), 12; https://doi.org/10.3390/jvd5020012 - 28 Feb 2026
Cited by 1 | Viewed by 1055
Abstract
Background: Human immunodeficiency virus (HIV) and antiretroviral therapy (ART) are known to be involved in cardiovascular disease development. They act alongside systemic risk factors, which interact with both macrovascular and microvascular vessels to accelerate vascular damage. Therefore, the aim of this study was [...] Read more.
Background: Human immunodeficiency virus (HIV) and antiretroviral therapy (ART) are known to be involved in cardiovascular disease development. They act alongside systemic risk factors, which interact with both macrovascular and microvascular vessels to accelerate vascular damage. Therefore, the aim of this study was to investigate the cardiovascular risk factors and their relationship with retinal microvascular function in HIV-positive pregnant women on ART in Mthatha, South Africa. Methods: A cross-sectional study was carried out among 78 pregnant women (25 HIV-positive and 53 HIV-negative) in Mthatha, South Africa. Blood pressure (BP) parameters, including systolic BP (SBP), diastolic BP (DBP), and heart rate (HR), were measured, and mean arterial pressure (MAP) was calculated. Lipid profile parameters and fasting blood glucose were assessed. Markers for kidney function, such as albuminuria, were determined. Vascular biomarkers including asymmetric dimethyl arginine (ADMA) and human endothelial specific molecule-1 were quantified. Non-invasive vascular function parameters such as flow-mediated slowing (FMS), carotid-femoral pulse wave velocity (cfPWV), ankle-brachial index, central retinal arteriolar equivalent (CRAE), central retinal venular equivalent (CRVE), arteriolar venular ratio (AVR), uterine artery pulsatile index (UtA PI) were determined. Results: Diastolic BP, MAP, cfPWV, ADMA, low density lipoprotein (LDL-c) and UtA PI were higher in the HIV-positive group (p ≤ 0.05) compared to the HIV-negative group. The prevalence of prehypertension/hypertension was higher in the HIV-positive group (p ≤ 0.05). DBP, MAP, and cfPWV correlated positively with CRVE in the HIV-positive group (p ≤ 0.05), while AVR negatively correlated with the urinary creatinine (uCr) in the same group (p ≤ 0.05). Linear regression results demonstrated that DBP, cfPWV, ABI, and LDL-c were predictors of reduced AVR in the HIV-positive group. Conclusions: Increased cardiovascular risk was observed in HIV-positive pregnant women on ART. Further, increased cardiovascular risk such as hypertension and endothelial dysfunction due to ART predicted retinal microvascular dysfunction in the HIV-positive population. This implies a potential mechanistic link between macrovascular dysfunction due to cardiovascular risk factors and retinal microvascular impairment, highlighting the importance of assessing cardiovascular risk early and preserving overall vascular health in HIV-positive population. Full article
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15 pages, 2806 KB  
Article
The Complete Mitochondrial Genome of Portunion sinensis (Crustacea: Isopoda) and Its Phylogenies
by Teng Huang, Xiaowan Ma, Shengping Zhong, Jie Chen, Dewei Cheng, Xuyang Chen, Dong Yang, Lixing Huang, Theerakamol Pengsakul, Ying Qiao and Wenhong Li
Biology 2026, 15(3), 282; https://doi.org/10.3390/biology15030282 - 4 Feb 2026
Viewed by 1023
Abstract
In this study, we conducted molecular identification and complete mitochondrial genome annotation of isopod parasites isolated from mud crabs (Scylla paramamosain) in the China Sea. The specimen was identified as Portunion sinensis, a recently described species of the family Entoniscidae. [...] Read more.
In this study, we conducted molecular identification and complete mitochondrial genome annotation of isopod parasites isolated from mud crabs (Scylla paramamosain) in the China Sea. The specimen was identified as Portunion sinensis, a recently described species of the family Entoniscidae. P. sinensis is characterized by an anterior thorax positioned vertically and posterior ventral processes directed backwards; the female’s marsupium is formed by the close adhesion of oostegites to the host membrane; the first oostegite is differentiated into three parts; the pleopoda have well-developed lamellar and pleural lamellae; and two ventral ovarian processes are present along with a pair of dorsal processes. The complete mitochondrial genome of the parasite is 14,603 bp in length, containing 35 genes (13 protein-coding genes, 20 transfer RNAs, and 2 ribosomal RNAs) as well as a putative control region (CR) located between the cob and nad1 genes. This study represents the initial characterization of the mitochondrial genome of P. sinensis. These findings provide molecular validation of its status as an independent species and lay the groundwork for the future identification of parasites within the genus Portunion. These data provide a necessary molecular reference for future research into the systematics and evolutionary history of decapod-infesting parasites. Full article
(This article belongs to the Section Marine and Freshwater Biology)
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21 pages, 5324 KB  
Article
Mitogenomic Characterization, Genetic Diversity, and Matrilineal Phylogenetic Insights of the Marbled Goby (Oxyeleotris marmorata) from Its Native Range in Indonesia
by Sarifah Aini, Angkasa Putra, Hye-Eun Kang, Mira Maulita, Sang Van Vu, Hyun-Woo Kim, Kyoungmi Kang and Shantanu Kundu
Int. J. Mol. Sci. 2026, 27(1), 140; https://doi.org/10.3390/ijms27010140 - 22 Dec 2025
Cited by 4 | Viewed by 1786
Abstract
Butidae is a family of teleost fishes with diverse morphological and ecological adaptations, including the marbled goby (Oxyeleotris marmorata), a large species of high economic value in Southeast and East Asia. The previous mitogenomic studies on cultured populations of O. marmorata [...] Read more.
Butidae is a family of teleost fishes with diverse morphological and ecological adaptations, including the marbled goby (Oxyeleotris marmorata), a large species of high economic value in Southeast and East Asia. The previous mitogenomic studies on cultured populations of O. marmorata from non-native habitats have provided limited insights into genetic divergence, structural variation, and evolutionary relationships. Hence, this study presented the complete mitochondrial genome of O. marmorata from its native habitat in Indonesia, providing structural characterization, assessment of genetic diversity, and matrilineal phylogenetic analysis. The circular mitogenome was 16,525 bp, comprising 37 genes and a non-coding control region (CR). The gene organization and strand distribution were conserved among Oxyeleotris species, with 28 genes on the heavy strand and nine on the light strand, and a pronounced A+T compositional bias. The comparative analyses of O. marmorata (from both native and cultured habitats) and Oxyeleotris lineolata mitogenomes revealed minor variations in intergenic spacers, gene overlaps, protein-coding gene (PCGs) lengths, and codon usage patterns. Conversely, the nonsynonymous and synonymous substitution ratios observed in species of the family Butidae and its closest related family (Eleotridae) indicate strong purifying selection in the present dataset. Notably, the ATG was the predominant start codon, whereas the COI gene utilized GTG, and amino acid composition analysis demonstrated high frequencies of arginine, leucine, and serine. Most transfer RNAs retained the canonical cloverleaf secondary structure except for trnS1, which lacked a functional dihydrouridine arm, whereas the CR contained four conserved sequence blocks with variable nucleotide motifs and no detectable tandem repeats. The haplotype analysis of native (Indonesia) and introduced populations (China) highlighted three haplotypes with high diversity (Hd = 1.0000) and substantial nucleotide variation (π = 0.6667). The genetic divergence across 13 PCGs was gene-specific, with COI and ND5 showing the highest variation, while ND4L and ATP8 were highly conserved. The phylogenetic analyses based on concatenated 13 PCGs using both Bayesian Inference and Maximum Likelihood methods revealed that Oxyeleotris forms a monophyletic clade and is closely related to Bostrychus sinensis. In addition, the broader phylogenetic framework inferred the matrilineal relationships within the family Butidae and its closest related family, Eleotridae. This study also recommends expanding analyses to include the mitogenomes of the remaining 17 Oxyeleotris species, together with comprehensive genomic data, to further elucidate their genetic architecture, evolutionary history, and ecological adaptability across diverse aquatic ecosystems. Full article
(This article belongs to the Special Issue Molecular Insights into Zoology)
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22 pages, 5658 KB  
Article
Research on the Spatio-Temporal Evolution and Dynamic Prediction of Agricultural Carbon Emission Efficiency: A Case Study of 24 Counties in the Dabie Mountain Region of China
by Yuxuan Huang, Guanghui Zhao and Kexin Zhu
Sustainability 2026, 18(1), 122; https://doi.org/10.3390/su18010122 - 22 Dec 2025
Cited by 1 | Viewed by 744
Abstract
Agriculture has become a major source of greenhouse gases in China. Agricultural carbon emission efficiency (AECC), as a key indicator of agricultural greening and sustainability, holds significant importance for advancing synergistic pollution reduction and carbon emission reduction in China and implementing the “dual [...] Read more.
Agriculture has become a major source of greenhouse gases in China. Agricultural carbon emission efficiency (AECC), as a key indicator of agricultural greening and sustainability, holds significant importance for advancing synergistic pollution reduction and carbon emission reduction in China and implementing the “dual carbon” strategy in China, also providing ideas for agricultural emission reduction in developing countries around the world. Taking 24 counties (cities/districts) in the Dabie Mountains, a typical traditional agricultural mountainous region in central China that is currently facing agricultural green transformation, as the research objects, this study constructed an AECC measurement index system, collected 2010–2022 data, used a super-efficiency SBM model with undesirable outputs under the CRS mode to measure AECC, analyzed its spatiotemporal evolution, and applied a BP neural network for dynamic prediction. Our results show the following: (1) during the study period, Dabie Mountains’ overall AECC was low with fluctuations, showing significant but low-dispersion spatial differences; (2) temporally, the overall AECC showed an upward trend over the years, though the distribution pattern remained relatively dispersed; (3) spatially, a prominent “core-periphery” structure exists, with high-value areas showing a trend of spreading from block-like to patch-like, while overall spatial disparities converged; (4) in the coming years, the AECC in the Dabie Mountains will rise significantly with steady growth and shrinking spatial differences, and the spatial pattern will evolve into a “bipolar → tripolar → multipolar” structure. Full article
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35 pages, 4736 KB  
Article
Artificial Intelligence-Based Oil Well Condition Diagnosis and Production Parameter Optimization
by Lu Jia, Guowei Shi, Nengji Jiang, Shunquan Hu, Guangya Li and Zhipeng Zhang
Processes 2025, 13(12), 3872; https://doi.org/10.3390/pr13123872 - 1 Dec 2025
Viewed by 1377
Abstract
To address the challenges of low production efficiency, high energy consumption, and frequent equipment failures in low-producing wells, this study proposes an intelligent production parameter optimization method based on deep learning and multi-indicator fusion. First, a Long short-term memory (LSTM)-based prediction model was [...] Read more.
To address the challenges of low production efficiency, high energy consumption, and frequent equipment failures in low-producing wells, this study proposes an intelligent production parameter optimization method based on deep learning and multi-indicator fusion. First, a Long short-term memory (LSTM)-based prediction model was developed using the displacement–load characteristics of pumping-unit dynamometer cards. The results show that the model achieves an average prediction metric Q = 0.08, outperforming Back Propagation and Recurrent Neutral Network (BP and RNN) models. Second, a Convolutional Neutral Network (CNN) was employed to extract the fluid supply capability features, achieving a recognition accuracy exceeding 98%, thereby validating the model’s effectiveness. Combined with three types of time series data (liquid supply degree, dynamic liquid level, and liquid production rate), a multi-index fusion parameter optimization method is proposed. A comprehensive decision-making model is constructed based on the Analytic Hierarchy Process (AHP), which takes long-term, short-term, and overall feature changes as the basis, and forms a hierarchical framework by decomposing objectives and quantifying feature weights. The consistency ratio (CR) of the model is less than 0.1, meeting the requirement of logical consistency and enabling the output of standardized regulation suggestions. Consequently, a closed-loop system of “data preprocessing—condition prediction—state identification—parameter optimization” was constructed, enabling early dynamometer card prediction, accurate fluid supply fluctuation identification, and automatic generation of optimization schemes. This system effectively enhances production efficiency and equipment stability in low-producing wells, providing a technical foundation for intelligent oilfield development. Full article
(This article belongs to the Section AI-Enabled Process Engineering)
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15 pages, 10415 KB  
Article
Genetic Identity of the Red-legged Partridge (Alectoris rufa, Phasianidae) from the Island of Madeira
by Monica Guerrini, Hans-Martin Berg, Sylke Frahnert, Manuel Biscoito and Filippo Barbanera
Birds 2025, 6(4), 59; https://doi.org/10.3390/birds6040059 - 5 Nov 2025
Viewed by 2433
Abstract
The Red-legged Partridge (Alectoris rufa, Phasianidae) is a non-migrant gamebird endemic to southwestern Europe that was introduced into Mediterranean and Atlantic islands in historical times. This is the case for Madeira, Portugal, where a population morphologically assigned to A. r. hispanica [...] Read more.
The Red-legged Partridge (Alectoris rufa, Phasianidae) is a non-migrant gamebird endemic to southwestern Europe that was introduced into Mediterranean and Atlantic islands in historical times. This is the case for Madeira, Portugal, where a population morphologically assigned to A. r. hispanica has been present since the XV century. We assessed its genetic identity using 2248 (Cytochrome-b, Cyt-b + Control Region, CR) and 297 bp-long (CR) mitochondrial DNA sequences obtained from modern and archival (1900–1964, including Caccabis rufa maderensis syntypes) partridges, respectively. These sequences were compared against an already published dataset covering the entire Iberian A. rufa range. We found that all the haplotypes of modern birds from Madeira were private to this island. The putative subspecies was confirmed, and northern Portugal with northwestern Spain turned out to host the closest mainland populations. This result was in line with the origin of the first human settlers of Madeira from, among other historical provinces, Douro Litoral and Minho, the latter neighboring Galicia. Despite relatively recent A. rufa importations from continental Europe, we did not find any significant change over time in the haplotypic pattern of Madeiran partridges as well as any evidence for maternal introgression from species such as the congeneric Chukar Partridge (A. chukar). Studies relying on genome-wide markers and including the only captive-bred population of Madeira are needed to gain more comprehensive information for the management of the local A. rufa. Full article
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13 pages, 2429 KB  
Article
Mitochondrial Genome Features and Phylogenetic Analyses of Four Chrysochroinae Species (Coleoptera: Buprestidae)
by Jieqiong Wang, Yingying Li, Zhonghua Wei and Aimin Shi
Biomolecules 2025, 15(11), 1531; https://doi.org/10.3390/biom15111531 - 30 Oct 2025
Viewed by 898
Abstract
The number of known mitochondrial genomes in Buprestidae is limited, especially in Chrysochroinae, which seriously hinders the phylogenetic study of this family. The mitogenomes of Capnodis miliaris, Lamprodila cupreosplendens, Sphenoptera insidiosa and Philocteanus rubroaureus were sequenced, assembled and annotated in this [...] Read more.
The number of known mitochondrial genomes in Buprestidae is limited, especially in Chrysochroinae, which seriously hinders the phylogenetic study of this family. The mitogenomes of Capnodis miliaris, Lamprodila cupreosplendens, Sphenoptera insidiosa and Philocteanus rubroaureus were sequenced, assembled and annotated in this study. The mitogenomes of these four species are typical circular double-stranded DNA molecules, containing 13 protein-coding genes (PCGS), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (CR). The total lengths of these four mitogenomes are moderate, ranging from 15,778 bp to 16,230 bp. Additionally, their A + T content ranges from 68.76% to 73.47%, showing positive AT-skew values ranging from 0.098 to 0.181. Relative Synonymous Codon Usage (RSCU) analysis indicated that TTT (Phe), ATT (Ile), TCT (Ser2), and TTA (Leu2) are the most frequently used codons. The gene arrangement of four mitogenomes is consistent with the previously reported Buprestidae mitogenomes. Most of the PCGs use ATN as the start codon, with TAA as the stop codon or an incomplete stop codon T-. Phylogenetic trees were constructed based on the PCGs and rRNAs using both maximum-likelihood and Bayesian inference methods. The phylogenetic results showed that Julodinae, Polycestinae, Buprestinae and Agrilinae are monophyletic groups, and Chrysochroinae is a paraphyletic group. As the number of Buprestidae mitogenomes used for polyogenetic analysis increases, the topology of phylogenetic tree shows differences compared to previous studies. Full article
(This article belongs to the Section Molecular Biology)
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26 pages, 2586 KB  
Article
Equilibrium Dynamics in the CR3BP with Radiating Primary and Oblate Secondary Using the Rotating Mass Dipole Model
by Angela E. Perdiou, Aguda Ekele Vincent, Jagadish Singh and Vassilis S. Kalantonis
Mathematics 2025, 13(19), 3179; https://doi.org/10.3390/math13193179 - 3 Oct 2025
Cited by 1 | Viewed by 1524
Abstract
In this study, we numerically investigate the equilibrium dynamics of a rotating system consisting of two masses connected by a massless rod within the framework of the circular restricted three-body problem. The larger primary is modeled as a radiating body and the smaller [...] Read more.
In this study, we numerically investigate the equilibrium dynamics of a rotating system consisting of two masses connected by a massless rod within the framework of the circular restricted three-body problem. The larger primary is modeled as a radiating body and the smaller as an oblate spheroid. We explore the influence of the involved parameters, i.e., mass ratio (μ), force ratio (k), radiation pressure factor (q1), and oblateness coefficient (A2), on the number, positions, and linear stability of equilibrium points. Zero velocity curves are presented in the equatorial plane for varying values of the Jacobi constant. Up to five equilibrium points are identified of which three are collinear (L1, L2, L3) and two are non-collinear (L4, L5). The positions of all equilibria shift under variations in the perturbing parameters. While the collinear points are generally unstable, L1 can exhibit stability for certain combinations of μ, k, and q1. The non-collinear points may also be stable under specific conditions with stability zones expanding with increased parameter values. The model is applied to the irregular, elongated asteroid 951 Gaspra, for which five equilibrium points are found. Despite positional dependence on oblateness and radiation, the perturbations do not significantly affect the equilibrium points’ stability and the motion near them remains linearly unstable. The Lyapunov families of periodic orbits emanating from the collinear equilibria of this particular system are also investigated. Full article
(This article belongs to the Section C2: Dynamical Systems)
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19 pages, 3913 KB  
Article
The CRISPR-Cas9 System in Entamoeba histolytica Trophozoites: ehcp112 Gene Knockout and Effects on Other Genes in the V1 Virulence Locus
by Luz Virginia Reyes, Guillermina García-Rivera, Rosario Javier-Reyna, Edgar Morales-Rios, Sergio Tinajero, Cecilia Bañuelos, Daniel Talamás-Lara and Esther Orozco
Microorganisms 2025, 13(9), 2219; https://doi.org/10.3390/microorganisms13092219 - 22 Sep 2025
Viewed by 2362
Abstract
Gene editing enables a better understanding of protein functions. The genome of the protozoan parasite Entamoeba histolytica contains a 4500 bp DNA fragment comprising the ehcp112, ehadh, and ehrabb genes, which together form the V1 virulence locus. Studying these genes has [...] Read more.
Gene editing enables a better understanding of protein functions. The genome of the protozoan parasite Entamoeba histolytica contains a 4500 bp DNA fragment comprising the ehcp112, ehadh, and ehrabb genes, which together form the V1 virulence locus. Studying these genes has been challenging due to the lack of suitable methodologies. Here, we report the first in vitro and in vivo knockout in E. histolytica (ehcp112 gene) using a modified CRISPR-Cas9 strategy and explore its effects on the other V1 locus genes. Confocal and transmission electron microscopy were used to detect the RNP pathway formed by the Cas9 enzyme and the crRNA–tracrRNA complex, from their entry into the trophozoites until their arrival at the nucleus and heterochromatin. Scanning electron microscopy revealed that the mutant cells (EhCP112-KO) were smaller, with fewer pseudopodia and plasma membrane depressions. DNA sequencing and RT-qPCR assays identified a four-base deletion in the ehcp112 gene in the mutant trophozoites. Western blot assays of EhCP112-KO extracts revealed the absence of the EhCP112 protein. While the EhCP112-KO lysates digested gelatin more efficiently than the HM1:IMSS extracts, their secreted products showed poor enzymatic activity. The ehcp112 knockout also affected the transcription of the ehadh and ehrabb genes, probably due to their genomic position. In conclusion, the implementation of the CRISPR-Cas9 strategy in E. histolytica evidenced the coordinated expression of the ehcp112 gene and the other members of the V1 locus. Full article
(This article belongs to the Special Issue Advances in Molecular Biology of Entamoeba histolytica)
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23 pages, 4336 KB  
Article
Characterization of the Complete Mitogenome of Polypedates braueri (Anura, Rhacophoridae, Polypedates) and Insights into the Phylogenetic Relationships of Rhacophoridae
by Simin Chen, Huiling Huang, Siqi Shan, Chengmin Li, Kaiyuan Huang, Xinyi Xu and Lichun Jiang
Biology 2025, 14(9), 1299; https://doi.org/10.3390/biology14091299 - 20 Sep 2025
Cited by 1 | Viewed by 1225
Abstract
White-lipped tree frogs, Polypedates braueri, are currently included in the list of terrestrial wildlife with important ecological, scientific, and social value in China. Understanding the structure and characteristics of the mitochondrial genome provides essential information for resource conservation and phylogenetic analyses of [...] Read more.
White-lipped tree frogs, Polypedates braueri, are currently included in the list of terrestrial wildlife with important ecological, scientific, and social value in China. Understanding the structure and characteristics of the mitochondrial genome provides essential information for resource conservation and phylogenetic analyses of P. braueri. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of P. braueri has received little attention. In this paper, we analyzed the characterization of the mitochondrial genome of P. braueri and investigated the phylogenetic relationships of Rhacophoridae. The complete mitochondrial genome of P. braueri was 20,254 bp in length, containing thirty-six genes (twelve protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)), three non-coding regions for the origin of light strand (OL), and two control regions (CR). There were six overlapping regions and seventeen intergenic spacer regions in the mitogenome. The mitogenome also showed a bias towards A + T content (61.87%) and had negative AT-skew (−0.039) and GC-skew (−0.209). All the PCGs employed the ATG, ATA, or ATT as the start codon and TAA, TAG, AGG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1, which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that Rhacophoridae could be classified into four monophyletic genera. The phylogenetic status of P. braueri was closely related to that of Polypedates megacephalus and Polypedates leucomystax. Additionally, selective pressure analysis suggested that COX1 and ND1 were highly efficient for discriminating closely related species in the genus Polypedates, while ND4L was the most appropriate marker for population-level genetic analyses. The diversification of the Polypedates commenced during the Late Oligocene and extended into the Miocene. The present study provides valuable genomic information on P. braueri and new insights into the phylogenetic relationships of Rhacophoridae. Full article
(This article belongs to the Special Issue Progress in Wildlife Conservation, Management and Biological Research)
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