Search Results (1,157)

The recent discovery of TIGR-Tas (Tandem Interspaced Guide RNA–Targeting Systems) marks a major advance in the field of genome editing, introducing a new class of compact, programmable DNA-targeting systems that function independently of traditional CRISPR-Cas pathways. TIGR-Tas effectors use a novel dual-spacer guide RNA (tigRNA) to recognize both strands of target DNA without requiring a protospacer adjacent motif (PAM). These Tas proteins introduce double-stranded DNA cuts with characteristic 8-nucleotide 3′ overhangs and are significantly smaller than Cas9, offering delivery advantages for in vivo editing. Structural analyses reveal homology to box C/D snoRNP proteins, suggesting a previously unrecognized evolutionary lineage of RNA-guided nucleases. This review positions TIGR-Tas at the forefront of a new wave of RNA-programmable genome-editing technologies. In parallel, I provide comparative insight into the diverse and increasingly modular CRISPR-Cas systems, including Cas9, Cas12, Cas13, and emerging effectors like Cas3, Cas10, CasΦ, and Cas14. While the CRISPR-Cas universe has revolutionized molecular biology, TIGR-Tas systems open a complementary and potentially more versatile path for programmable genome manipulation. I discuss mechanistic distinctions, evolutionary implications, and potential applications in human cells, synthetic biology, and therapeutic genome engineering. Full article

The Millard’s rat (Dacnomys millardi), a threatened murid endemic to Southeast Asian montane rainforests and the sole member of its monotypic genus, faces escalating endangered risks as a Near Threatened species in China’s Biodiversity Red List. This ecologically specialized rodent exhibits diagnostic morphological adaptations—hypertrophied upper molars and cryptic pelage—that underpin niche differentiation in undisturbed tropical/subtropical forests. Despite its evolutionary distinctiveness, the conservation prioritization given to Dacnomys is hindered due to a deficiency of data and unresolved phylogenetic relationships. Here, we integrated morphological analyses with the first complete mitogenome (16,289 bp in size; no structural rearrangements) of D. millardi to validate its phylogenetic placement within the subfamily Murinae and provide novel insights into genetic diversity erosion. Bayesian and maximum likelihood phylogenies robustly supported Dacnomys as sister to Leopoldamys (PP = 1.0; BS = 100%), with an early Pliocene divergence (~4.8 Mya, 95% HPD: 3.65–5.47 Mya). Additionally, based on its basal phylogenetic position within Murinae, we propose reclassifying Micromys from Rattini to the tribe Micromyini. Codon usage bias analyses revealed pervasive purifying selection (Ka/Ks < 1), constraining mitogenome evolution. Genetic diversity analyses showed low genetic variation (CYTB: π = 0.0135 ± 0.0023; COX1: π = 0.0101 ± 0.0025) in fragmented populations. We propose three new insights into this genetic diversity erosion. (1) Evolutionary constraints: genome-wide evolutionary conservation and shallow evolutionary history (~4.8 Mya) limited mutation accumulation. (2) Anthropogenic pressures: deforestation-driven fragmentation of habitats (>20,000 km²/year loss since 2000) has reduced effective population size, exacerbating genetic drift. (3) Ecological specialization: long-term adaptation to stable niches favored genomic optimization over adaptive flexibility. These findings necessitate suitable conservation action by enforcing protection of core habitats to prevent deforestation-driven population collapses and advocating IUCN reclassification of D. millardi from Data Deficient to Near Threatened. Full article

Amidst the intensification of global climate change and the increasing impacts of human activities, ecosystem patterns and processes have undergone substantial transformations. The distribution and evolutionary dynamics of mountain ecosystems have become a focal point in ecological research. The Surkhan River Basin is located in the transitional zone between the arid inland regions of Central Asia and the mountain systems, where its unique physical and geographical conditions have shaped distinct patterns of vertical zonation. Utilizing Landsat imagery, this study applies a hierarchical classification approach to derive land cover classifications within the Surkhan River Basin. By integrating the NDVI (normalized difference vegetation index) and DEM (digital elevation model (30 m SRTM)), an “NDVI-DEM-Land Cover” scatterplot is constructed to analyze zonation characteristics from 1980 to 2020. The 2020 results indicate that the elevation boundary between the temperate desert and mountain grassland zones is 1100 m, while the boundary between the alpine cushion vegetation zone and the ice/snow zone is 3770 m. Furthermore, leveraging DEM and LST (land surface temperature) data, a potential energy analysis model is employed to quantify potential energy differentials between adjacent zones, enabling the identification of ecological transition areas. The potential energy analysis further refines the transition zone characteristics, indicating that the transition zone between the temperate desert and mountain grassland zones spans 1078–1139 m with a boundary at 1110 m, while the transition between the alpine cushion vegetation and ice/snow zones spans 3729–3824 m with a boundary at 3768 m. Cross-validation with scatterplot results confirms that the scatterplot analysis effectively delineates stable zonation boundaries with strong spatiotemporal consistency. Moreover, the potential energy analysis offers deeper insights into ecological transition zones, providing refined boundary identification. The integration of these two approaches addresses the dimensional limitations of traditional vertical zonation studies, offering a transferable methodological framework for mountain ecosystem research. Full article

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

As distant hybridization has profound implications for evolutionary biology, aquaculture, and biodiversity conservation, this study aims to elucidate patterns of maternal inheritance, genetic divergence, and phylogenetic relationships by synthesizing mitochondrial genome (mitogenome) data from 74 distant hybrid fish species. These hybrids span diverse taxa, including 48 freshwater and 26 marine species, with a focus on Cyprinidae (n = 35) and Epinephelus (n = 14), representing the most frequently hybridized groups in freshwater and marine systems, respectively. Mitogenome lengths were highly conserved (15,973 to 17,114 bp); however, the genetic distances between hybrids and maternal species varied from 0.001 to 0.17, with 19 hybrids (25.7%) showing distances >0.02. Variable sites in these hybrids were randomly distributed but enriched in hypervariable regions, such as the D-loop and NADH dehydrogenase subunits 1, 3 and 6 (ND2, ND3, and ND6) genes, likely reflecting maternal inheritance (reported in Cyprinus carpio × Carassius auratus). Moreover, these genes were under purifying selection pressure, revealing their conserved nature. Phylogenetic reconstruction using complete mitogenomes revealed three distinct clades in hybrids: (1) Acipenseriformes, (2) a freshwater cluster dominated by Cypriniformes and Siluriformes, and (3) a marine cluster comprising Centrarchiformes, Pleuronectiformes, Scombriformes, Cichliformes, Anabantiformes, Tetraodontiformes, Perciformes, and Salmoniformes. The prevalence of Cyprinidae hybrids underscores their importance in aquaculture for hybridization, where traits such as rapid growth and disease resistance are enhanced. In contrast, marine hybrids are valued for their market value and adaptability. While mitogenome data robustly support maternal inheritance in most cases, exceptions suggest complex mechanisms, such as doubly uniparental inheritance (DUI), in distantly related crosses. Moreover, AT-skew of genes in hybrids revealed a paternal leakage of traits in mitogenomes. This study also highlights ecological risks, such as genetic swamping in native populations, emphasizing the need for responsible hybridization practices. These findings advance our understanding of the role of hybridization in fish evolution and aquaculture, providing a genomic framework and policy recommendations for optimizing breeding programs, hybrid introduction, and mitigating conservation challenges. Full article

This study introduces a novel tripartite evolutionary game model to analyze the strategic interactions among electric vehicle (EV) aggregators, local governments, and EV users in vehicle–grid interaction (VGI) markets. The core novelty lies in capturing bounded rationality and dynamic decision-making across the three stakeholders, revealing how policy incentives and market mechanisms drive the transition from disordered charging to bidirectional VGI. Key findings include the following: (1) The system exhibits five stable equilibrium points, corresponding to three distinct developmental phases of the VGI market: disordered charging (V0G), unidirectional VGI (V1G), and bidirectional VGI (V2G). (2) Peak–valley price differences are the primary driver for transitioning from V0G to V1G. (3) EV aggregators’ willingness to adopt V2G is influenced by upgrade costs, while local governments’ subsidy strategies depend on peak-shaving benefits and regulatory costs. (4) Increasing the subsidy differential between V1G and V2G accelerates market evolution toward V2G. The framework offers actionable policy insights for sustainable VGI development, while advancing evolutionary game theory applications in energy systems. Full article

This study investigates strategies for urban-scale renewable energy integration through a photovoltaic-centric approach, with a case study of a district in Barcelona. The methodology integrates spatial and morphological data using a geographic information system (GIS)-based and clustering framework to address challenges of CO₂ emissions, air pollution, and energy inefficiency. Rooftop availability and photovoltaic (PV) design constraints are analysed under current urban regulations. The spatial analysis incorporates building geometry and solar exposure, while an evolutionary optimisation algorithm in Grasshopper refines shading analysis, energy yield, and financial performance. Clustering methods (K-means and 3D proximity) group PV panels by solar irradiance uniformity and spatial coherence to enhance system efficiency. Eight PV deployment scenarios are evaluated, incorporating submodule integrated converter technology under a solar power purchase agreement model. Results show distinct trade-offs among PV scenarios. The standard fixed tilted (31.5° tilt, south-facing) scenario offers a top environmental and performance ratio (PR) = 66.81% but limited financial returns. In contrast, large- and huge-sized modules offer peak financial returns, aligning with private-sector priorities but with moderate energy efficiency. Medium- and large-size scenarios provide balanced outcomes, while a small module and its optimised rotated version scenarios maximise energy output yet suffer from high capital costs. A hybrid strategy combining standard fixed tilted with medium and large modules balances environmental and economic goals. The district’s morphology supports “solar neighbourhoods” and demonstrates how multi-scenario evaluation can guide resilient PV planning in Mediterranean cities. Full article

The germin-like protein (GLP) family plays vital roles for plant growth, stress adaptation, and defense; however, its evolutionary dynamics and functional diversity in halophytes remain poorly characterized. Here, we present the genome-wide analysis of the GLP family in the halophytic forage alkaligrass (Puccinellia tenuiflora), which identified 54 PutGLPs with a significant expansion compared to other plant species. Phylogenetic analysis revealed monocot-specific clustering, with 41.5% of PutGLPs densely localized to chromosome 7, suggesting tandem duplication as a key driver of family expansion. Collinearity analysis confirmed evolutionary conservation with monocot GLPs. Integrated gene structure and motif analysis revealed conserved cupin domains (BoxB and BoxC). Promoter cis-acting elements analysis revealed stress-responsive architectures dominated by ABRE, STRE, and G-box motifs. Tissue-/organ-specific expression profiling identified root- and flower-enriched PutGLPs, implying specialized roles in stress adaptation. Dynamic expression patterns under salt-dominated stresses revealed distinct regulatory pathways governing ionic and alkaline stress responses. Functional characterization of PutGLP37 demonstrated its cell wall localization, dual superoxide dismutase (SOD) and oxalate oxidase (OXO) enzymatic activities, and salt stress tolerance in Escherichia coli, yeast (Saccharomyces cerevisiae INVSc1), and transgenic Arabidopsis. This study provides critical insights into the evolutionary innovation and stress adaptive roles of GLPs in halophytes. Full article

The Southern Lhasa Terrane, as the southernmost tectonic unit of the Eurasian continent, has long been a focal area in global geoscientific research due to its complex evolutionary history. The Yeba Formation exposed in this terrane comprises an Early–Middle Jurassic volcanic–sedimentary sequence that records multiphase tectonic deformation. This study applies structural analysis to identify three distinct phases of tectonic deformation in the Yeba Formation of the Southern Lhasa Terrane. The D₁ deformation is characterized by brittle–ductile shearing, as evidenced by the development of E-W-trending regional shear foliation (S₁). S₁ planes dip northward at angles of 27–87°, accompanied by steeply plunging stretching lineations (85–105°). Both south- and north-directed shear-rotated porphyroclasts are observed in the hanging wall. ⁴⁰Ar-³⁹Ar dating results suggest that the D₁ deformation occurred at ~79 Ma and may represent an extrusion-related structure formed under a back-arc compressional regime induced by the low-angle subduction of the Neo-Tethys Ocean plate. The D₂ deformation is marked by the folding of the pre-existing shear foliation (S₁), generating an axial planar cleavage (S₂). S₂ planes dip north or south with angles of 40–70° and fold hinges plunge westward or NWW. Based on regional tectonic evolution, it is inferred that the deformation may have resulted from sustained north–south compressional stress during the Late Cretaceous (79–70 Ma), which caused the overall upward extrusion of the southern Gangdese back-arc basin, leading to upper crustal shortening and thickening and subsequently initiating folding. The D₃ deformation is dominated by E-W-striking ductile shear zones. The regional shear foliation (S₃) exhibits a preferred orientation of 347°∠75°. Outcrop-scale ductile deformation indicators reveal a top-to-the-NW shear sense. Combined with regional tectonic evolution, the third-phase (D3) deformation is interpreted as a combined product of the transition from compression to lateral extension within the Lhasa terrane, associated with the activation of the Gangdese Central Thrust (GCT) and the uplift of the Gangdese batholith since ~25 Ma. Full article

This study identifies and classifies resistance gene analogues (RGAs) in the genomes of Brassica nigra, Sinapis arvensis and Sinapis alba using the RGAugury pipeline. RGAs were categorised into four main classes: receptor-like kinases (RLKs), receptor-like proteins (RLPs), nucleotide-binding leucine-rich repeat (NLR) proteins and transmembrane-coiled-coil (TM-CC) genes. A total of 4499 candidate RGAs were detected, with species-specific proportions. RLKs were the most abundant across all genomes, followed by TM-CCs and RLPs. The sub-classification of RLKs and RLPs identified LRR-RLKs, LRR-RLPs, LysM-RLKs, and LysM-RLPs. Atypical NLRs were more frequent than typical ones in all species. Atypical NLRs were more frequent than typical ones in all species. We explored the relationship between chromosome size and RGA count using regression analysis. In B. nigra and S. arvensis, larger chromosomes generally harboured more RGAs, while S. alba displayed the opposite trend. Exceptions were observed in all species, where some larger chromosomes contained fewer RGAs in B. nigra and S. arvensis, or more RGAs in S. alba. The distribution and density of RGAs across chromosomes were examined. RGA distribution was skewed towards chromosomal ends, with patterns differing across RGA types. Sequence hierarchical pairwise similarity analysis revealed distinct gene clusters, suggesting evolutionary relationships. The study also identified homologous genes among RGAs and non-RGAs in each species, providing insights into disease resistance mechanisms. Finally, RLKs and RLPs were co-localised with reported disease resistance loci in Brassica, indicating significant associations. Phylogenetic analysis of cloned RGAs and QTL-mapped RLKs and RLPs identified distinct clusters, enhancing our understanding of their evolutionary trajectories. These findings provide a comprehensive view of RGA diversity and genomics in these Brassicaceae species, providing valuable insights for future research in plant disease resistance and crop improvement. Full article

Nitrogen use efficiency remains the primary bottleneck for sustainable maize production. This study elucidates the functional mechanisms of the amino acid transporter ZmAAP1 in nitrogen absorption and stress resilience. Through systematic evolutionary analysis of 55 maize inbred lines, we discovered that the ZmAAP1 gene family exhibits distinct chromosomal localization (Chr7 and Chr9) and functional domain diversification (e.g., group 10-specific motifs 11/12), indicating species-specific adaptive evolution. Integrative analysis of promoter cis-elements and multi-omics data confirmed the root-preferential expression of ZmAAP1 under drought stress, mediated via the ABA-DRE signaling pathway. To validate its biological role, we generated transgenic maize lines expressing Arabidopsis thaliana AtAAP1 via Agrobacterium-mediated transformation. Three generations of genetic stability screening confirmed the stable genomic integration and root-specific accumulation of the AtAAP1 protein (Southern blot/Western blot). Field trials demonstrated that low-N conditions enhanced the following transgenic traits: the chlorophyll content increased by 13.5%, and the aboveground biomass improved by 7.2%. Under high-N regimes, the gene-pyramided hybrid ZD958 (AAP1 + AAP1) achieved a 12.3% yield advantage over conventional varieties. Our findings reveal ZmAAP1’s dual role in root development and long-distance nitrogen transport, establishing it as a pivotal target for molecular breeding. This study provides actionable genetic resources for enhancing NUE in maize production systems. Full article

Sacrificial rituals provide a critical perspective for examining the fundamental characteristics and evolutionary trajectory of Chinese civilization. The Functionalist and Annales schools, through theoretical frameworks such as “natural necessity theory” and “social-centric theory”, have explored the origins of sacrificial practices and their role in social cohesion. When these schools investigate Chinese sacrificial rituals, they identify significant differences in the humanistic and ethical dimensions compared to in Western intellectual traditions, thereby revealing how these distinctions propelled China onto a unique civilizational path. The sacrificial system underwent a process of humanization and moralization during the Shang and Zhou dynasties, culminating in the recognition of benevolence–righteousness attributes within human nature, primarily characterized by affection and reverence. The interplay between intrinsic human dispositions and ritualized sacrificial practices established the foundational structure for the social order, spanning from familial units to political society in China. This synthesis ultimately shaped the distinctive philosophical characteristics of Chinese civilization, emphasizing the principles of benevolent love, reciprocal loyalty, and harmonious coexistence. Full article

Dopaminergic amacrine cells (DACs) are a subclass of amacrine cells that modulate retinal processing and light adaptation by releasing dopamine. Although the role of dopamine is largely conserved, their retinal distribution across mammals remains incompletely characterized. In mice, rats, thirteen-lined ground squirrels (TLGSs), and macaques, we systematically compared the localization, number, and topography of DACs by their expression of tyrosine hydroxylase (TH), a crucial enzyme in the biosynthesis of dopamine. In all species examined, TH+ cells were primarily located in the inner nuclear layer; however, there was a species-dependent influence on their number and distribution. Mice exhibited the highest density of TH+cells but completely lacked displaced TH+cells (dTH+cells) in the ganglion cell layer. Despite interspecies variation in the total number of TH+cells in the retina, the overall density in rats, TLGSs, and macaques was similar. Most species displayed a higher density of DACs toward central retinal regions. However, rats exhibited a distinctive dorsal concentration, particularly among dTH+cells. Although most species examined exhibited a similar ratio of TH+cells to Brn3a+ retinal ganglion cells, TLGSs showed a marked reduction, indicating a potentially diminished dopaminergic modulatory role. Species-specific DAC topographies aligned with specialized visual regions, such as the visual streak in TLGS and the macula in macaques. These results reveal both conserved and divergent features of retinal dopamine circuitry, reflecting evolutionary adaptations to visual processing demands. Full article

The largest Eurasian rodent, the Eurasian beaver Castor fiber, is known for its amphibious lifestyle that allows it to adapt its environment to its needs. Due to its lifestyle and evolutionary history, the beaver is characterized by a distinct, unique parasitofauna. In this context, the occurrence of mites from the Demodecidae family in the Eurasian beaver was investigated. The topography of the Demodex castoris was analyzed: it was previously known from a single record from a single skin location of this host. The mite was found in large numbers in various locations in the hairy skin, including the head, trunk, and limbs. In addition, a new species associated with hairless skin, mainly around the mouth, was discovered and described: Demodex ovaportans sp. nov. The females of this species carry the egg on the dorsal side of the podosoma, which may be a form of care and a previously unknown reproductive strategy in Demodecidae. Our findings confirm that a host-specific demodecid mite species associated with the hairy skin of the entire body is a universal model in mammals. They also emphasize the uniqueness of the beaver parasitofauna, as evidenced by the host specificity and the different biology of the demodecids described in it. Full article

The Tsushima leopard cat (Prionailurus bengalensis euptilurus), an endangered feline endemic to Tsushima Island, Japan, faces critical threats due to its small and isolated population. Understanding its demographic history and genetic differentiation from continental populations is essential for conservation planning. In this study, we performed whole-genome sequencing of four Tsushima individuals and applied demographic inference methods, including pairwise sequentially Markovian coalescent (PSMC) and Sequentially Markovian Coalescent (SMC++), to reconstruct the historical effective population size (Ne) and estimate divergence times. PSMC revealed a population expansion between 200,000 and 100,000 years ago, followed by a long-term decline. SMC++ inferred a continuous decline and estimated that the divergence from the Korean leopard cat population occurred approximately 30,000–20,000 years ago. Genetic diversity analysis showed that the Tsushima population has significantly lower heterozygosity and higher inbreeding levels than continental populations. Genetic clustering based on genome-wide SNPs indicated that the Tsushima population is genetically closest to the Korean population, forming a northern cluster distinct from southern populations, such as Borneo and the Malay Peninsula. These findings provide valuable insights into the evolutionary history and genetic status of the Tsushima leopard cat and contribute critical data for the design of future conservation strategies targeting this unique insular lineage. Full article