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Mingfang Zhang, Sally Mackenzie and colleagues report the genome sequence of allopolyploid Brassica juncea and through comparative analysis suggest that A-subgenome evolution contributes to differences in agricultural subvarieties. They find that differential homoeolog gene expression from the subgenomes helps to shape the selection that distinguishes vegetable- and oil-use Brassica . The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-molecule reads integrated to genomic and genetic maps. We discovered that the A subgenomes of B. juncea and Brassica napus each had independent origins. Results suggested that A subgenomes of B. juncea were of monophyletic origin and evolved into vegetable-use and oil-use subvarieties. Homoeolog expression dominance occurs between subgenomes of allopolyploid B . juncea , in which differentially expressed genes display more selection potential than neutral genes. Homoeolog expression dominance in B . juncea has facilitated selection of glucosinolate and lipid metabolism genes in subvarieties used as vegetables and for oil production. These homoeolog expression dominance relationships among Brassicaceae genomes have contributed to selection response, predicting the directional effects of selection in a polyploid crop genome.

The dysregulation of extracellular matrix (ECM) metabolism and autophagy in chondrocytes is central to osteoarthritis (OA) pathogenesis, yet the molecular mechanisms remain poorly defined. Ubiquitin-specific protease 15 (USP15), a key modulator of TGF-β/Smad2/3 signaling through TβR-I stabilization, may play a critical role in maintaining chondrocyte homeostasis. We conducted in vitro and ex vivo experiments using OA patient-derived cartilage samples and chondrocyte models to test the hypotheses that (1) USP15 deficiency exacerbates OA progression by impairing TGF-β/Smad2/3 signaling, leading to ECM degradation and autophagy dysfunction; and (2) restoring USP15 expression activates this pathway to mitigate cartilage degeneration, an effect reversible by TGF-β/Smad inhibition. Lentiviral-mediated USP15 knockdown or overexpression, combined with pharmacological inhibition assays, revealed that reduced USP15 levels in OA lesions correlated with disease severity (Kellgren-Lawrence grading) and triggered ECM catabolism (downregulated Col-II, MMP-13), suppressed autophagy (reduced LC3-II, accumulated p62), and increased apoptosis. Conversely, USP15 overexpression stabilized TβR-I, enhanced TGF-β/Smad2/3 signaling activity, increased Smad2/3 protein expression and promoted Smad2/3 phosphorylation( p  < 0.01), and restored ECM synthesis and autophagic flux. These protective effects were abolished by the TGF-β receptor kinase inhibitor SIS3 ( p  < 0.001), confirming pathway dependency. Our findings establish USP15 as a pivotal regulator of chondrocyte homeostasis via the TβR-I/Smad axis, offering novel therapeutic targets for OA intervention.

Objective Ferritin heavy chain 1 (FTH1) is an important subunit of ferro-storing proteins and is indispensable for iron metabolism. Though it has been extensively studied in numerous organs and diseases, the relationship between FTH1 and osteoarthritis (OA) is unclear. Design Primary murine chondrocytes and cartilage explants were treated with FTH1 siRNA for 72 h. Mice were injected with adenovirus expressing FTH1 after destabilized medial meniscus (DMM) surgery. These approaches were used to determine the effect of FTH1 expression on the pathophysiology of OA. Results FTH1 expression was down regulated in OA patients and mice after DMM surgery. Knock down of FTH1 induced articular cartilage damage and extracellular matrix degradation in cartilage explants. Further, over expression of FTH1 reduced the susceptibility of chondrocytes to ferroptosis and reversed decrements in SOX9 and aggrecan after DMM surgery. Moreover, FTH1 relieved OA by inhibition of the chondrocyte MAPK pathway. Conclusion This study found FTH1 to play an essential role in extracellular matrix degradation, ferroptosis, and chondrocytes senescence during OA progression. Further, injection of adenovirus expressing FTH1 may be a potential strategy for OA prevention and therapy.

Brassica rapa comprises several important cultivated vegetables and oil crops. Current reference genome assemblies of Brassica rapa are quite fragmented and not highly contiguous, thereby limiting extensive genetic and genomic analyses. Here, we report an improved assembly of the B. rapa genome (v3.0) using single-molecule sequencing, optical mapping, and chromosome conformation capture technologies (Hi-C). Relative to the previous reference genomes, our assembly features a contig N50 size of 1.45 Mb, representing a ~30-fold improvement. We also identified a new event that occurred in the B. rapa genome ~1.2 million years ago, when a long terminal repeat retrotransposon (LTR-RT) expanded. Further analysis refined the relationship of genome blocks and accurately located the centromeres in the B. rapa genome. The B. rapa genome v3.0 will serve as an important community resource for future genetic and genomic studies in B. rapa . This resource will facilitate breeding efforts in B. rapa , as well as comparative genomic analysis with other Brassica species. Genomes: a new map of field mustard A detailed third-generation genome sequence has been published for Brassica rapa , which includes crops such as napa cabbage, turnips, and bok choy. Older technologies required researchers to stitch together many short sequences. Recently developed methods produce long, high-fidelity sequences. Xiaowu Wang at the Chinese Academy of Agricultural Science and the Shandong Provincial Key Laboratory of Protected Vegetable Molecular Breeding, Hongkun Zheng at Biomarker Technologies Corporation, and coworkers in China assembled the new version using 1498 sequences, compared to the 96,883 needed for the previous version. These methods provide a significant improvement in the level of detail, and permit mapping of highly repetitive regions, which were nearly impossible to map using older methods. The new sequence will aid breeding efforts, permit better comparisons with other Brassica genomes, and improve our understanding of genome evolution.

This study investigates the deposition of tantalum (Ta) coatings on carbon foams using the chemical vapor deposition (CVD) method to enhance their compressive strength. Two types of open-cell carbon foams, CF-1 and CF-2, with different strut diameters, were examined. The morphology and uniformity of the coatings were characterized, and the effect of coating thickness on the compressive strength of the foams was systematically analyzed. An empirical model was proposed and successfully validated, showing that the compressive strength is proportional to the coating thickness and the square of the strut diameter. The experimental results demonstrate that considering mass transfer and reaction kinetics can significantly improve the uniformity of coatings on larger substrates. Furthermore, the Ta coatings significantly increased the compressive strength of the foams, with the relationship between compressive strength, coating thickness, and strut diameter being in good agreement with the predictions of the proposed model. The study highlights the potential of tailored metallic coatings to enhance the mechanical properties of porous materials while maintaining their lightweight characteristics, emphasizing the importance of optimizing coating parameters for large-scale applications.

The interplay between insertion sequences (ISs) and antibiotic resistance genes (ARGs) in Acinetobacter baumannii contributes to resistance against specific antibiotics. Conventionally, genetic variations and ARGs have been utilized for predicting resistance phenotypes, with the potential pivotal role of IS elements largely overlooked. Our study advances this approach by integrating both rule-based and machine learning models to predict AMR in A. baumannii . This significantly enhances the accuracy of AMR prediction, emphasizing the pivotal function of IS elements in antibiotic resistance. Notably, we uncover a series of conserved sequence patterns linking IS elements and ARGs, which outperform ARGs alone in phenotypic prediction. Our findings are crucial for bioinformatics strategies aimed at studying and tracking AMR, offering novel insights into combating the escalating AMR challenge.

We present multiPrime, a novel tool that automatically designs minimal primer sets for targeted next‐generation sequencing, tailored to specific microbiomes or genes. MultiPrime enhances primer coverage by designing primers with mismatch tolerance and ensures both high compatibility and specificity. We evaluated the performance of multiPrime using a data set of 43,016 sequences from eight viruses. Our results demonstrated that multiPrime outperformed conventional tools, and the primer set designed by multiPrime successfully amplified the target amplicons. Furthermore, we expanded the application of multiPrime to 30 types of viruses and validated the work efficacy of multiPrime‐designed primers in 80 clinical specimens. The subsequent sequencing outcomes from these primers indicated a sensitivity of 94% and a specificity of 89%. This study introduces multiPrime, a novel tool tailored for the wide‐ranging detection of target sequences through targeted next‐generation sequencing (tNGS). By integrating degenerate primer design principles with effective mismatch handling, multiPrime demonstrates enhanced precision and specificity in the identification of diverse sequence types. This breakthrough presents a prospective pathway for optimizing the development of tNGS. In performance comparison, multiPrime excelled over conventional tools in terms of execution time, primer coverage, and the number of candidate primers. It offers a streamlined and versatile solution for the rapid and cost‐effective detection of diverse microbiomes. Highlights MultiPrime is a user‐friendly and one‐step tool for designing targeted next‐generation sequencing primer sets. It integrates degenerate primer design theory with mismatch handling, resulting in improved accuracy and specificity in detecting broad‐spectrum sequences. It outperformed conventional programs in terms of run time, primer number, and primer coverage. The versatility and potential of multiPrime are highlighted by its potential application in detecting single or multiple genes, exons, antisense strands, RNA, or other specific DNA segments.

infections in humans typically result in symptoms such as abdominal pain and diarrhea. When the diarrhea is severe, it can cause serious complications and even be life-threatening, especially in patients with compromised immune systems. Here, we reported the use of metagenomic next-generation sequencing (mNGS) to assist in the diagnosis and treatment of a 10-year-old boy with severe infection. Despite the absence of any history of immunocompromise, the infection still resulted in severe symptoms, including shock, as well as damage to his pancreas and kidneys. The mNGS tests detected the presence of when conventional methods failed. The patient received anti-parasite treatment along with supportive care to manage the condition. With disease surveillance based on regular clinical tests and sequential mNGS tests, the child recovered from the severe conditions. Our study emphasized the importance of recognizing the potential severity of infection, even among individuals with normal immune systems. Timely diagnosis and ongoing monitoring are essential for patient prognosis.

The advancement of urban rail transit is increasingly confronted with environmental challenges related to vibration and noise. To investigate the critical issues surrounding vibration propagation and the generation of structure-borne noise, a two-story frame building was selected for on-site measurements of both vibration and its induced structure-borne noise. The collected data were analyzed in both the time and frequency domains to explore the correlation between these phenomena, leading to the proposal of a hybrid prediction method for structural noise that was subsequently compared with measured results. The findings indicate that the excitation of structure-borne noise produces significant waveforms within sound signals. The characteristic frequency of the structure-borne noise is 25–80 Hz, as well as that of the train-induced vibration. Furthermore, there exists a positive correlation between structural vibration and structure-borne noise, whereby increased levels of vibration correspond to more pronounced structure-borne noise; additionally, indoor distribution patterns of structure-borne noise are non-uniform, with corner wall areas exhibiting greater intensity than central room locations. Finally, a hybrid prediction methodology that is both semi-analytical and semi-empirical is introduced. The approach derives dynamic response predictions of the structure through analytical solutions, subsequently estimating the secondary noise within the building’s interior using a newly formulated empirical equation to facilitate rapid predictions regarding indoor building vibrations and structure-borne noises induced by subway train operations.

Like many important crops, peanut is a polyploid that underwent polyploidization, evolution, and domestication. The wild allotetraploid peanut species Arachis monticola (A. monticola) is an important and unique link from the wild diploid species to cultivated tetraploid species in the Arachis lineage. However, little is known about A. monticola and its role in the evolution and domestication of this important crop. A fully annotated sequence of ≈2.6 Gb A. monticola genome and comparative genomics of the Arachis species is reported. Genomic reconstruction of 17 wild diploids from AA, BB, EE, KK, and CC groups and 30 tetraploids demonstrates a monophyletic origin of A and B subgenomes in allotetraploid peanuts. The wild and cultivated tetraploids undergo asymmetric subgenome evolution, including homoeologous exchanges, homoeolog expression bias, and structural variation (SV), leading to subgenome functional divergence during peanut domestication. Significantly, SV‐associated homoeologs tend to show expression bias and correlation with pod size increase from diploids to wild and cultivated tetraploids. Moreover, genomic analysis of disease resistance genes shows the unique alleles present in the wild peanut can be introduced into breeding programs to improve some resistance traits in the cultivated peanuts. These genomic resources are valuable for studying polyploid genome evolution, domestication, and improvement of peanut production and resistance. The wild allotetraploid peanut species Arachis monticola (A. monticola) is an important and unique link from the wild diploid species to cultivated tetraploid species in the Arachis lineage. A fully annotated sequence of the A. monticola genome and comparative genomics of Arachis species are presented, which reveals asymmetric subgenome evolution and genome‐assisted improvement of peanut production and resistance.