Search Results (129)

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

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 ($\mu$), force ratio (k), radiation pressure factor ($q_1$), and oblateness coefficient ($A_2$), 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 ($L_1$, $L_2$, $L_3$) and two are non-collinear ($L_4$, $L_5$). The positions of all equilibria shift under variations in the perturbing parameters. While the collinear points are generally unstable, $L_1$ can exhibit stability for certain combinations of $\mu$, k, and $q_1$. 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

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

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 (O_L), 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

Clonorchis sinensis, a parasitic liver fluke, is the primary aetiological agent of clonorchiasis, a disease predominantly characterized by liver-related clinical manifestations. Currently, research on the complete mitochondrial (mt) genome of local C. sinensis populations remains inadequate. Thus, in this study, we sequenced and annotated the mt genome of fish-borne C. sinensis (Cs-c2) from Changchun, Jilin Province, China, a strain not previously described. This mt genome is 14,136 bp in length and harbours 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a single control region (CR). We constructed a maximum likelihood (ML) phylogenetic tree using concatenated ND5, ND6, and ND1 from protein-coding genes (PCGs) of the C. sinensis mitochondrial genome (mt genome). This tree more clearly differentiated C. sinensis strains from three geographical regions (China, Russia, and South Korea) and distinguished Opisthorchiidae from two closely related families (Fasciolidae and Dicrocoeliidae). Additionally, we constructed an ML phylogenetic tree using concatenated ND4, ND5, ND1, ND2, and COX1 from the PCGs of digenean (Digenea) mt genomes. This approach—utilizing multiple high-resolution PCGs with evolutionary rates distinct from those of the mt genome—yielded robust clustering for multiple suborders and 13 families within Digenea and provided new molecular evidence for intergeneric relationships within the suborder Plagiorchiata of Digenea. These findings serve as important references for future research on the differentiation of closely related geographical strains of digeneans, as well as for studies on molecular taxonomy and population genetics. Full article

Neurodegeneration is increasingly recognized not as a linear trajectory of protein accumulation, but as a multidimensional collapse of biological organization—spanning intracellular signaling, transcriptional identity, proteostatic integrity, organelle communication, and network-level computation. This review intends to synthesize emerging frameworks that reposition neurodegenerative diseases (ND) as progressive breakdowns of interpretive cellular logic, rather than mere terminal consequences of protein aggregation or synaptic attrition. The discussion aims to provide a detailed mapping of how critical signaling pathways—including PI3K–AKT–mTOR, MAPK, Wnt/β-catenin, and integrated stress response cascades—undergo spatial and temporal disintegration. Special attention is directed toward the roles of RNA-binding proteins (e.g., TDP-43, FUS, ELAVL2), m6A epitranscriptomic modifiers (METTL3, YTHDF1, IGF2BP1), and non-canonical post-translational modifications (SUMOylation, crotonylation) in disrupting translation fidelity, proteostasis, and subcellular targeting. At the organelle level, the review seeks to highlight how the failure of ribosome-associated quality control (RQC), autophagosome–lysosome fusion machinery (STX17, SNAP29), and mitochondrial import/export systems (TIM/TOM complexes) generates cumulative stress and impairs neuronal triage. These dysfunctions are compounded by mitochondrial protease overload (LONP1, CLPP), UPR maladaptation, and phase-transitioned stress granules that sequester nucleocytoplasmic transport proteins and ribosomal subunits, especially in ALS and FTD contexts. Synaptic disassembly is treated not only as a downstream event, but as an early tipping point, driven by impaired PSD scaffolding, aberrant endosomal recycling (Rab5, Rab11), complement-mediated pruning (C1q/C3–CR3 axis), and excitatory–inhibitory imbalance linked to parvalbumin interneuron decay. Using insights from single-cell and spatial transcriptomics, the review illustrates how regional vulnerability to proteostatic and metabolic stress converges with signaling noise to produce entropic attractor collapse within core networks such as the DMN, SN, and FPCN. By framing neurodegeneration as an active loss of cellular and network “meaning-making”—a collapse of coordinated signal interpretation, triage prioritization, and adaptive response—the review aims to support a more integrative conceptual model. In this context, therapeutic direction may shift from damage containment toward restoring high-dimensional neuronal agency, via strategies that include the following elements: reprogrammable proteome-targeting agents (e.g., PROTACs), engineered autophagy adaptors, CRISPR-based BDNF enhancers, mitochondrial gatekeeping stabilizers, and glial-exosome neuroengineering. This synthesis intends to offer a translational scaffold for viewing neurodegeneration as not only a disorder of accumulation but as a systems-level failure of cellular reasoning—a perspective that may inform future efforts in resilience-based intervention and precision neurorestoration. Full article

Background and Objectives: The clinical value of HER2-low breast cancer (BC), defined by immunohistochemistry (IHC) scores of 1+ or 2+/ISH-negative without HER2 amplification, remains unclear in the neoadjuvant setting. This study aimed to determine whether HER2-low and HER2-zero tumors differ in pathological complete response (pCR) rates and disease-free survival (DFS) among early-stage breast cancer patients undergoing neoadjuvant chemotherapy (NAC). Materials and Methods: We retrospectively analyzed 134 early BC patients treated with NAC between 2017 and 2023. Patients were categorized as HER2-zero (IHC 0) or HER2-low (IHC 1+ or 2+/ISH–). The primary endpoint was total pCR (tpCR); secondary endpoints included breast (bpCR), nodal (npCR), and radiologic complete response (rCR), alongside DFS analysis stratified by hormone receptor (HR) status. Results: Of the cohort, 91 patients (67.9%) were HER2-zero and 43 (32.1%) were HER2-low. There was no statistically significant difference in tpCR (26.4% vs. 27.9%, p = 0.852), bpCR (28.6% vs. 30.2%, p = 0.843), npCR (37.4% vs. 32.6%, p = 0.588), and rCR (23.1% vs. 30.2%, p = 0.374) between HER2-zero and HER2-low groups. DFS did not significantly differ between HER2-zero and HER2-low groups overall (p = 0.714), nor within HR-positive (p = 0.540) or TNBC (p = 0.523) subgroups. Conclusions: HER2-low tumors demonstrated similar pathological responses and survival outcomes compared to HER2-zero tumors. While a HER2-low status does not appear to define a distinct biological subtype in early BC, it remains a relevant classification for emerging HER2-targeted therapies, needing further investigation in prospective studies. Full article

Tarantulas represent a highly diverse taxonomic group and play a crucial role in ecosystems. To gain a deeper understanding of the evolutionary relationships within the family Theraphosidae, in this study, we characterized the mitochondrial genome (mitogenome) of Phormictopus cancerides for the first time. The mitogenome is a typical circular double-stranded molecule, with a size of 13,776 bp. P. cancerides exhibited an A/T nucleotide preference (61.9–68.5% A + T content), with their rRNAs and tRNAs showing higher values than PCGs and the CR. The genes and the gene order were consistent with other Theraphosidae mitogenomes. The mitogenome was compacted and showed a bias for A/T. Ka/Ks analyses showed that the ND3 gene had the highest evolutionary rate, while the COX1 gene displayed a relatively slower evolution. Our phylogenetic analysis based on mitogenomes showed the subfamily Theraphosinae is closely related to the subfamily Harpactirinae and the subfamily Selenocosmiinae. Our results could contribute to the study of relationships within the family Theraphosidae and lay the foundation for further studies on tarantulas. Full article

This paper investigates the design of optimal low-thrust transfers between relative planar and spatial quasi-satellite orbits (QSOs) in the Earth–Moon system under the Circular Restricted Three-Body Problem (CR3BP). A key contribution is the adaptation of a trajectory optimization framework, previously applied to halo orbit transfers, to accommodate the unique challenges of QSO families, especially the transition between planar and spatial configurations. The method employs a refined beam search strategy to construct diverse initial guess chains, which are then optimized via a successive convexification algorithm tailored for the spatial dynamics of QSOs. Additionally, a linear–quadratic regulator (LQR)-based control scheme is implemented to ensure long-term station-keeping of the final 3D-QSO. Simulation results demonstrate the feasibility of connecting planar and spatial QSOs with minimum-fuel trajectories while maintaining bounded terminal deviations, offering new tools for future Earth–Moon logistics and navigation infrastructure. Key findings include the successful design of low-thrust transfer trajectories between planar QSOs and 1:5 3D-QSOs, with a minimum total $\mathsf{\Delta }V$ of 195.576 m/s over a time of flight (ToF) of 261 days, and a minimum ToF of 41 days with a total $\mathsf{\Delta }V$ of 270.507 m/s. Additionally, the application of LQR control demonstrated the ability to maintain 1:5 3D-QSO families around the Moon with less than 12 mm/s $\mathsf{\Delta }V$ over two months. This research provides valuable insights into the optimization of low-thrust transfer trajectories and the application of advanced control techniques for space missions, particularly those targeting lunar and planetary satellite exploration. Full article

Background: Lonchodidae is the largest family within the order Phasmatodea, and although many studies have been conducted on this family, the monophyly of the family has not been established. Methods: Eight mitogenomes from Lonchodidae, including the first complete mitogenomes of four genera, were sequenced and annotated to explore their features and phylogenetic relationships. Results: The total length ranged from 15,942–18,021 bp, and the mitogenome consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region (CR). atp8 had the highest A + T content in Lonchodidae, except for Neohirasea stephanus and Asceles clavatus, in which the highest A + T contents were detected in nad6. The phylogenetic trees were reconstructed via Bayesian inference (BI) and maximum likelihood (ML) based on the PCG123 and PCG12 datasets. As the phylogenetic trees show, Necrosciinae is recognized as monophyletic, but the monophyly of Lonchodinae has not been supported. Gene deletion and rearrangement have occurred mainly in Lonchodidae and Aschiphasmatidae. The most common reason for gene rearrangements was tandem duplication random loss (TDRL), but trnI of Stheneboea repudiosa inverted into the CR. In addition, genes within the same family or genus share related sequences and conserved gene blocks. Conclusions: we expanded the mitochondrial genomic data for this family, thereby establishing a foundational dataset for future studies. Full article

Background: Ptinidae, within the infraorder Bostrichiformia, are a cosmopolitan, ecologically diverse but poorly known group. The phylogeny within Bostrichiformia and the monophyly of Ptinidae and its phylogenetic placement in Bostrichiformia remain contentious. Methods: In this research, we determined the entire mitochondrial genome (mitogenome) of Gibbium aequinoctiale, the first representative mitogenome of the subfamily Ptininae, and reconstructed the phylogenetic relationships for Bostrichiformia based on four mitochondrial datasets using maximum likelihood (ML) and Bayesian inference (BI) methods. Results: The mitogenome of G. aequinoctiale is a circular molecule spanning 17,020 bp and harbors 37 mitochondrial genes and a presumed control region (CR). The mitogenome exhibited a marked preference for the utilization of A and T bases, which was also observed in three kinds of genes and CR. AAT was inferred as the putative candidate initiation codon for cytochrome oxidase subunits 1 (COI). The control region contains three tandem repeats (TDRs) and one poly-thymine stretch (Poly-T) in both coding strands. The phylogenetic results appeared to support the monophyly of four families, Nosodendridae, Derodontidae, Dermestidae, and Bostrichidae, and the basal position of the latter two families within Bostrichiformia. However, the family Ptinidae was not verified as monophyly because of one species diverging from the main lineage. Three families, Dermestidae, Bostrichidae, and Ptinidae, clustered as the major clade in Bostrichiformia, among which Bostrichidae and Ptinidae grouped together as sister groups. Conclusions: The present study provides valuable mitochondrial information for Ptinidae and provides novel perspectives on the inner phylogeny within the infraorder Bostrichiformia. Full article

In triple-negative (TNBC) and human epidermal growth factor receptor 2-positive (HER2+) breast cancer patients, neoadjuvant systemic therapy is the standard recommendation for tumors larger than 2 cm. Monitoring the response to primary systemic therapy allows for the assessment of treatment effects, the need for breast-conserving surgery (BCS), and the achievement of pathological complete responses (pCRs). In estrogen receptor-positive/HER2-negative (ER+/HER2-) breast cancer, the benefit of neoadjuvant strategies is controversial, as they have shown lower tumor downstaging and pCR rates compared to other breast cancers. In recent decades, several gene expression assays have been developed to tailor adjuvant treatments in ER+/HER2- early breast cancer (EBC) to identify the patients that will benefit the most from adjuvant chemotherapy (CT) and those at low risk who could be spared from undergoing CT. It is still a challenge to identify patients who will benefit from neoadjuvant systemic treatment (CT or endocrine therapy (ET)). Here, we review the published data on the most common gene expression signatures (MammaPrint (MP), BluePrint (BP), Oncotype Dx, PAM50, the Breast Cancer Index (BCI), and EndoPredict (EP)) and their ability to predict the response to neoadjuvant treatment, as well as the possibility of using them on core needle biopsies. Additionally, we review the changes in the gene expression signatures after neoadjuvant treatment, and the ongoing clinical trials related to the utility of gene expression signatures in the neoadjuvant setting. Full article

The opening of the Qiongzhou Strait during the Holocene was a significant geological event in the Beibu Gulf, profoundly influencing sediment provenance and ocean circulation systems. Due to the scarcity of geological records documenting this event, the understanding of regional Holocene sedimentary evolution has been constrained. To investigate the impact of this event on sediment provenance and ocean currents in the Beibu Gulf, geochemical analyses were conducted on sediment core SO-31 retrieved from the South China Sea. The sediments in core SO-31 were stratigraphically divided into three units based on vertical geochemical profiles, reflecting changes in sea level and shifts in sediment provenance within the study area. The Th/Cr vs. Th/Sc scatter plot for core SO-31 indicate that sedimentary materials primarily originated from the Red River during 11,400–7700 a BP, and a significant change in provenance occurred in the study region around 7700 a BP, characterized by increased contributions from the Qiongzhou Strait and decreased contributions from the Red River. This suggests that the opening of the Qiongzhou Strait significantly influenced the sediment supply to the central Beibu Gulf around 7700 a BP. These findings provide critical geochemical evidence for studying the Qiongzhou Strait opening event and enhance our understanding of Holocene sedimentary evolution and “source–sink” transitions in the Beibu Gulf. Full article

The lunar south pole has gained significant attention due to its unique scientific value and potential for supporting future human exploration. Its potential water ice reservoirs and favourable conditions for long-term habitation make it a strategic target for upcoming space missions. This has led to a continuous increase in missions towards the Moon thanks mainly to the boost provided by NASA’s Artemis programme. This study focuses on designing a satellite constellation to provide communication coverage for the lunar south pole. Among the various cislunar orbits analysed, the halo orbit families near Earth–Moon Lagrangian points L1 and L2 emerged as the most suitable ones for ensuring continuous communication while minimising the number of satellites required. These orbits, first described by Farquhar in 1966, allow spacecraft to maintain constant communication with Earth due to their unique geometric properties. The candidate orbits were initially implemented in MATLAB using the Circular Restricted Three-Body Problem (CR3BP) to analyse their main features such as stability, periodicity, and coverage time percentage. In order to develop a more detailed and realistic scenario, the obtained initial conditions were refined using a full ephemeris model, incorporating a ground station located near the Connecting Ridge Extension to evaluate communication performance depending on the minimum elevation angle of the antenna. Different multi-body constellations were propagated; however, the constellation consisting of three satellites around L2 and a single satellite around L1 turned out to be the one that best matches the coverage requirements. Full article

The color of maize grain, ranging from pink to purple, is related to the presence of phenolic compounds whose efficient extraction is affected by the solvent used. This study aimed to determine the effect of solvents and maize grain color on the phenolic composition and biological activities of maize extracts. Six samples (two with brick red, BR, two with cherry red CR, and two with blue–purple BP) of maize grain were used. The solvents were acidic methanol (MTFA) and aqueous acetone (AWAC). The phenolic composition was evaluated by total soluble phenolics (TSPs), anthocyanins (TACs), flavonoids (FLAVs), and proanthocyanidins (PAs). Biological activities evaluated were antioxidant capacity (AC), antifungal activity (AFA) and antimutagenic (AM) activity. The type of solvent used exerted a higher effect than the maize grain color on the phenolic composition of biological activities. The TAC and FLAV variables were more influenced by solvent than TSPs and PAs, while AC was affected only when evaluated by the DPPH method. AWAC extracts showed AFA and had the highest AM, unlike MTFA extracts. These results highlight the importance of selecting an appropriate solvent to maximize the functional properties of maize grain extracts and reach a more objective evaluation of the potential of food on its biological activities. Full article