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Muntjac deer have experienced drastic karyotype changes during their speciation, making it an ideal model for studying mechanisms and functional consequences of mammalian chromosome evolution. Here we generated chromosome-level genomes for Hydropotes inermis (2n = 70), Muntiacus reevesi (2n = 46), female and male M. crinifrons (2n = 8/9) and a contig-level genome for M. gongshanensis (2n = 8/9). These high-quality genomes combined with Hi-C data allowed us to reveal the evolution of 3D chromatin architectures during mammalian chromosome evolution. We find that the chromosome fusion events of muntjac species did not alter the A/B compartment structure and topologically associated domains near the fusion sites, but new chromatin interactions were gradually established across the fusion sites. The recently borne neo-Y chromosome of M. crinifrons , which underwent male-specific inversions, has dramatically restructured chromatin compartments, recapitulating the early evolution of canonical mammalian Y chromosomes. We also reveal that a complex structure containing unique centromeric satellite, truncated telomeric and palindrome repeats might have mediated muntjacs’ recurrent chromosome fusions. These results provide insights into the recurrent chromosome tandem fusion in muntjacs, early evolution of mammalian sex chromosomes, and reveal how chromosome rearrangements can reshape the 3D chromatin regulatory conformations during species evolution. Muntjac deer underwent rapid species radiation and dramatic chromosome fusions within a short period of time. Here the authors reveal that repeat sequences likely mediated illegitimate recombination to result in chromosome fusions and that 3D chromatin architecture around fusion sites have no significant change, while significant interactions across fusion sites were gradually established after speciation.

The advancements in intelligent action recognition can be instrumental in developing autonomous robotic systems capable of analyzing complex human activities in real-time, contributing to the growing field of robotics that operates in dynamic environments. The precise recognition of basketball players' actions using artificial intelligence technology can provide valuable assistance and guidance to athletes, coaches, and analysts, and can help referees make fairer decisions during games. However, unlike action recognition in simpler scenarios, the background in basketball is similar and complex, the differences between various actions are subtle, and lighting conditions are inconsistent, making action recognition in basketball a challenging task. To address this problem, an Adaptive Context-Aware Network (ACA-Net) for basketball player action recognition is proposed in this paper. It contains a Long Short-term Adaptive (LSTA) module and a Triplet Spatial-Channel Interaction (TSCI) module to extract effective features at the temporal, spatial, and channel levels. The LSTA module adaptively learns global and local temporal features of the video. The TSCI module enhances the feature representation by learning the interaction features between space and channels. We conducted extensive experiments on the popular basketball action recognition datasets SpaceJam and Basketball-51. The results show that ACA-Net outperforms the current mainstream methods, achieving 89.26% and 92.05% in terms of classification accuracy on the two datasets, respectively. ACA-Net's adaptable architecture also holds potential for real-world applications in autonomous robotics, where accurate recognition of complex human actions in unstructured environments is crucial for tasks such as automated game analysis, player performance evaluation, and enhanced interactive broadcasting experiences.

Aflatoxin B1 (AFB1) is one of the most commonly found mycotoxin in corn, which is highly toxic, carcinogenic, teratogenic, and mutagenic for the health of humans and animals. In order to reduce the AFB1 in corn, corn kernels were processed with Water-assisted Microwaves Treatment (WMT) and the feasibility of WMT processing on AFB1 reduction and its effects on corn quality were analyzed. Increasing the treatment time and microwave power could increase the reduction of AFB1, and the maximum reduction rate could reach 58.6% and 56.8%, respectively. There was no significant correlation between the initial concentration of AFB1 and the reduction rate of AFB1. During WMT, the main toxigenic molds were sterilized completely, and the moisture content of corn climbed up and then declined to the initial level. WMT could obviously increase the fatty acid value and pasting temperature of corn and reduce the all paste viscosity of corn. However, it had little effect on the color of corn. The results indicated that WMT could reduce AFB1 effectively and avoid the vast appearance of heat-damaged kernels simultaneously. Undoubtedly, water played an important role in WMT. This result provides a new idea for the reduction of AFB1 by microwave.

Cartilaginous fishes (e.g., sharks, rays, and skates) cannot see blue or violet light, potentially because they lack the shortwave-sensitive cone opsin gene ( sws ). Widespread gene loss can occur during evolution, but the evolutionary mechanisms underlying sws loss remains unclear. Here, we construct whole-genome assemblies of Okamejei kenojei (skate) and Prionace glauca (blue shark). We then analyze the distribution characteristics and intragroup differences of opsin-related genes in cartilaginous fishes. Using a zebrafish model with sws deleted we infer that in the presence of SWS1 and SWS2, blue and violet light respectively, can induce cell aging. This is followed by photoreceptor layer thinning, demonstrating, sws loss aids in preventing shortwave light damage to the eye. In the retinas of numerous cartilaginous fishes, the tapetum lucidum strongly reflects light. Therefore, in cartilaginous fish, the existence of tapetum lucidum in the retina and loss of sws may be interdependent; in other words, this adaptive gene loss may increase cartilaginous fish fitness. Cartilaginous fishes lost the short-wave-sensitive ( sws ) opsin genes at some point in their evolutionary history. Here, the authors present genome assemblies of Okamejei kenojei (skate) and Prionace glauca (blue shark) that confirm sws loss, together with experimental evidence that sws loss reduces shortwave light damage to the eye.

Snails at hydrothermal vents rely on symbiotic bacteria for nutrition; however, the specifics of these associations in adapting to such extreme environments remain underexplored. This study investigated the community structure and metabolic potential of bacteria associated with two Indian Ocean vent snails, Chrysomallon squamiferum and Gigantopelta aegis. Using microscopic, phylogenetic, and metagenomic analyses, this study examines bacterial communities inhabiting the foot and gland tissues of these snails. G. aegis exhibited exceptionally low bacterial diversity (Shannon index 0.14–0.18), primarily Gammaproteobacteria (99.9%), including chemosynthetic sulfur-oxidizing Chromatiales using Calvin–Benson–Bassham cycle and methane-oxidizing Methylococcales in the glands. C. squamiferum hosted significantly more diverse symbionts (Shannon indices 1.32–4.60). Its black variety scales were dominated by Campylobacterota (67.01–80.98%), such as Sulfurovum, which perform sulfur/hydrogen oxidation via the reductive tricarboxylic acid cycle, with both Campylobacterota and Gammaproteobacteria prevalent in the glands. The white-scaled variety of C. squamiferum had less Campylobacterota but a higher diversity of heterotrophic bacteria, including Delta-/Alpha-Proteobacteria, Bacteroidetes, and Firmicutes (classified as Desulfobacterota, Pseudomomonadota, Bacteroidota, and Bacillota in GTDB taxonomy). In C. squamiferum, Gammaproteobacteria, including Chromatiales, Thiotrichales, and a novel order “Endothiobacterales,” were chemosynthetic, capable of oxidizing sulfur, hydrogen, or iron, and utilizing the Calvin–Benson–Bassham cycle for carbon fixation. Heterotrophic Delta- and Alpha-Proteobacteria, Bacteroidetes, and Firmicutes potentially utilize organic matter from protein, starch, collagen, amino acids, thereby contributing to the holobiont community and host nutrition accessibility. The results indicate that host species and intra-species variation, rather than the immediate habitat, might shape the symbiotic microbial communities, crucial for the snails’ adaptation to vent ecosystems.

Sirenians of the superorder Afrotheria were the first mammals to transition from land to water and are the only herbivorous marine mammals. Here, we generated a chromosome-level dugong ( Dugong dugon ) genome. A comparison of our assembly with other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS ( SLC5A5 ) and its co-transporters. Functional in vitro assays confirm that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans. Our analysis also uncovers gene losses that may be maladaptive in a modern environment, including a candidate gene ( KCNK18 ) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break ~10.7 thousand years ago on the Australian east coast and provide evidence of an associated ecotype, and highlight the need for whole-genome resequencing data from dugong populations worldwide for conservation and genetic management. Sirenians are aquatic mammals that originated in Africa ~60 million years ago. Using comparative genomics of a new dugong genome, this study finds genetic adaptations shared by extant sirenians and assessed the diversity of dugongs in Australian waters and the functionally extinct Okinawan dugong.

Low-dose methotrexate (LD-MTX), a treatment regimen involving weekly doses ≤20 mg, is widely used in rheumatoid arthritis. Methotrexate (MTX) is primarily excreted via the kidneys. However, the assessment protocol for the adverse reaction risk threshold of the LD-MTX dosing regimen in renal impairment remains inadequate. This study aims to use pharmacovigilance analysis and physiologically-based pharmacokinetic (PBPK) model to combine the analysis of the risk of adverse reactions of LD-MTX in patients with renal impairment. Collected and analyzed disproportionate signals from adverse reaction reports on MTX in patients with renal impairment from the FDA Adverse Event Reporting System (FAERS) from Q1 2004 to Q3 2024. The restricted cubic spline (RCS) model explored the nonlinear relationship between MTX maximum plasma concentration and dose to derive risk thresholds. The PBPK model was developed and validated using MTX data in healthy adults, and further extended to chronic kidney disease (CKD) populations to simulate dose risks. FAERS analysis revealed heightened risks of hematological disorders, hepatic impairment, and pulmonary adverse events (AEs) with MTX in renal impairment. The optimized threshold based on RCS and the PBPK model simulation results indicated that the risk of adverse reactions increased starting from CKD stage 2. LD-MTX confers increased adverse reaction risks in renal impairment, notably from CKD stage 2 or higher, necessitating dose adjustments and vigilant monitoring.

Background Bivalves have independently evolved a variety of symbiotic relationships with chemosynthetic bacteria. These relationships range from endo- to extracellular interactions, making them ideal for studies on symbiosis-related evolution. It is still unclear whether there are universal patterns to symbiosis across bivalves. Here, we investigate the hologenome of an extracellular symbiotic thyasirid clam that represents the early stages of symbiosis evolution. Results We present a hologenome of Conchocele bisecta (Bivalvia: Thyasiridae) collected from deep-sea hydrothermal vents with extracellular symbionts, along with related ultrastructural evidence and expression data. Based on ultrastructural and sequencing evidence, only one dominant Thioglobaceae bacteria was densely aggregated in the large bacterial chambers of C. bisecta , and the bacterial genome shows nutritional complementarity and immune interactions with the host. Overall, gene family expansions may contribute to the symbiosis-related phenotypic variations in different bivalves. For instance, convergent expansions of gaseous substrate transport families in the endosymbiotic bivalves are absent in C. bisecta . Compared to endosymbiotic relatives, the thyasirid genome exhibits large-scale expansion in phagocytosis, which may facilitate symbiont digestion and account for extracellular symbiotic phenotypes. We also reveal that distinct immune system evolution, including expansion in lipopolysaccharide scavenging and contraction of IAP (inhibitor of apoptosis protein), may contribute to the different manners of bacterial virulence resistance in C. bisecta . Conclusions Thus, bivalves employ different pathways to adapt to the long-term co-existence with their bacterial symbionts, further highlighting the contribution of stochastic evolution to the independent gain of a symbiotic lifestyle in the lineage.

Background Coleoid cephalopods have distinctive neural and morphological characteristics compared to other invertebrates. Early studies reported massive genomic rearrangements occurred before the split of octopus and squid lineages (Proc Natl Acad Sci U S A 116:3030-5, 2019), which might be related to the neural innovations of their brain, yet the details remain elusive. Here we combine genomic and single-nucleus transcriptome analyses to investigate the octopod chromosome evolution and cerebral characteristics. Results We present a chromosome-level genome assembly of a gold-ringed octopus, Amphioctopus fangsiao , and a single-nucleus transcriptome of its supra-esophageal brain. Chromosome-level synteny analyses estimate that the chromosomes of the ancestral octopods experienced multiple chromosome fission/fusion and loss/gain events by comparing with the nautilus genome as outgroup, and that a conserved genome organization was detected during the evolutionary process from the last common octopod ancestor to their descendants. Besides, protocadherin, GPCR, and C2H2 ZNF genes are thought to be highly related to the neural innovations in cephalopods (Nature 524:220–4, 2015), and the chromosome analyses pinpointed several collinear modes of these genes on the octopod chromosomes, such as the collinearity between PCDH and C2H2 ZNF, as well as between GPCR and C2H2 ZNF. Phylogenetic analyses show that the expansion of the octopod protocadherin genes is driven by a tandem-duplication mechanism on one single chromosome, including two separate expansions at 65 million years ago (Ma) and 8–14 Ma, respectively. Furthermore, we identify eight cell types (i.e., cholinergic and glutamatergic neurons) in the supra-esophageal brain of A. fangsiao , and the single-cell expression analyses reveal the co-expression of protocadherin and GPCR in specific neural cells, which may contribute to the neural development and signal transductions in the octopod brain. Conclusions The octopod genome analyses reveal the dynamic evolutionary history of octopod chromosomes and neural-related gene families. The single-nucleus transcriptomes of the supra-esophageal brain indicate their cellular heterogeneities and functional interactions with other tissues (i.e., gill), which provides a foundation for further octopod cerebral studies.

A split grouting-reinforced body (SGRB) is the new surrounding rock that forms after split grouting reinforcement in tunnels and underground engineering, and its shear-seepage behavior is one of the critical factors affecting tunnel stability. The effects of seepage pressure, confining pressure, and the roughness of the soil–slurry interface on the shear-seepage characteristics of SGRB specimens were investigated using a modified triaxial shear-seepage coupling test system. The failure mechanism for the SGRB was analyzed taking into account its seepage behavior and mechanical characteristics. The results showed that the seepage process of the SGRB specimens could be divided into four stages according to the seepage velocity, including the waterless, rapid, decelerating, and steady seepage stages, and the corresponding water turbidity in the seepage stages was classified as turbid, mildly turbid, or clear, respectively. The peak shear stress of the soil–slurry interface of the SGRB specimens under seepage was lower than that in the waterless environment, and the peak shear stress decreased from 57.25 kPa (waterless) to 29.37 kPa (a seepage pressure of 0.08 MPa), marking a reduction of 50.74%. The seepage phenomenon of the specimens was related to the ‘seepage-to-confining ratio’, and its critical points in the waterless, seepage, and seepage surge stages were 0.2, 0.4, and 0.6, respectively.