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Hydrophiine sea snakes represent ecologically significant and species-rich marine predatory reptiles, many of which inhabit marine environments throughout their entire lifecycles. However, due to morphological variability and limited molecular phylogenetic studies, the taxonomic relationships within this group remain unclear. In this study, we present the first complete mitochondrial genome of Aipysurus sea snakes, specifically Aipysurus eydouxii Gray 1849. The mitogenome comprises 17,228 base pairs and contains a total of 37 genes, plus a putative control region. This study provides valuable genetic data that will contribute to the future taxonomic classification and ecological protection of hydrophiine sea snakes.

Abstract Photosystem I (PSI) from Fittonia albivenis, an Acanthaceae ornamental plant, is notable among green plants for its red-shifted emission spectrum. Here, we solved the structure of a PSI–light harvesting complex I (LHCI) supercomplex from F. albivenis at 2.46-Å resolution using cryo-electron microscopy. The supercomplex contains a core complex of 14 subunits and an LHCI belt with four antenna subunits (Lhca1–4) similar to previously reported angiosperm PSI–LHCI structures; however, Lhca3 differs in three regions surrounding a dimer of low-energy chlorophylls (Chls) termed red Chls, which absorb far-red beyond visible light. The unique amino acid sequences within these regions are exclusively shared by plants with strongly red-shifted fluorescence emission, suggesting candidate structural elements for regulating the energy state of red Chls. These results provide a structural basis for unraveling the mechanisms of light harvest and transfer in PSI–LHCI of under canopy plants and for designing Lhc to harness longer-wavelength light in the far-red spectral range.

Abstract Nanopore direct RNA sequencing (DRS) has emerged as a powerful tool for RNA modification identification. However, concurrently detecting multiple types of modifications in a single DRS sample remains a challenge. Here, we develop TandemMod, a transferable deep learning framework capable of detecting multiple types of RNA modifications in single DRS data. To train high-performance TandemMod models, we generate in vitro epitranscriptome datasets from cDNA libraries, containing thousands of transcripts labeled with various types of RNA modifications. We validate the performance of TandemMod on both in vitro transcripts and in vivo human cell lines, confirming its high accuracy for profiling m6A and m5C modification sites. Furthermore, we perform transfer learning for identifying other modifications such as m7G, Ψ, and inosine, significantly reducing training data size and running time without compromising performance. Finally, we apply TandemMod to identify 3 types of RNA modifications in rice grown in different environments, demonstrating its applicability across species and conditions. In summary, we provide a resource with ground-truth labels that can serve as benchmark datasets for nanopore-based modification identification methods, and TandemMod for identifying diverse RNA modifications using a single DRS sample.

Abstract Holothuria scabra, a commercially valuable yet ecologically vulnerable tropical holothuroid, has experienced a severe decline in its wild populations, especially in China. Genomic resources are crucial for the development of effective genomic breeding projects and stock conservation strategies to restore these natural populations. Until now, a high-quality, chromosome-level reference genome for H. scabra has not been available. Here, we employed Oxford Nanopore and Hi-C sequencing technologies to assemble and annotate a high-quality, chromosome-level reference genome of H. scabra. The final genome comprised 31 scaffolds with a total length of 1.19 Gb and a scaffold N50 length of 53.52 Mb. Remarkably, 1,191.67 Mb (99.95%) of the sequences were anchored to 23 pseudo-chromosomes, with the longest one spanning 79.75 Mb. A total of 34,418 protein-coding genes were annotated in the final genome, with BUSCO analysis revealing 98.01% coverage of metazoa_odb10 genes, marking a significant improvement compared to the previous report. These chromosome-level sequences and annotations will provide an essential genomic basis for further investigation into molecular breeding and conservation management of H. scabra.

Abstract Ditylenchus destructor is a migratory plant-parasitic nematode that severely harms many agriculturally important crops. The control of this pest is difficult, thus efficient strategies for its management in agricultural production are urgently required. Cathepsin L-like cysteine protease (CPL) is one important protease that has been shown to participate in various physiological and pathological processes. Here we decided to characterize the CPL gene (Dd-cpl-1) from D. destructor. Analysis of Dd-cpl-1 gene showed that Dd-cpl-1 gene contains a signal peptide, an I29 inhibitor domain with ERFNIN and GNFD motifs, and a peptidase C1 domain with four conserved active residues, showing evolutionary conservation with other nematode CPLs. RT-qPCR revealed that Dd-cpl-1 gene displayed high expression in third-stage juveniles (J3s) and female adults. In situ hybridization analysis demonstrated that Dd-cpl-1 was expressed in the digestive system and reproductive organs. Silencing Dd-cpl-1 in 1-cell stage eggs of D. destructor by RNAi resulted in a severely delay in development or even in abortive morphogenesis during embryogenesis. The RNAi-mediated silencing of Dd-cpl-1 in J2s and J3s resulted in a developmental arrest phenotype in J3 stage. In addition, silencing Dd-cpl-1 gene expression in female adults led to a 57.43% decrease in egg production. Finally, Dd-cpl-1 RNAi-treated nematodes showed a significant reduction in host colonization and infection. Overall, our results indicate that Dd-CPL-1 plays multiple roles in D. destructor ontogenesis and could serve as a new potential target for controlling D. destructor.

Helical growth of the root tip (circumnutation) that permits surface exploration facilitates root penetration into soil. Here, we reveal that rice actin-binding protein RMD aids in root circumnutation, manifested by wavy roots as well as compromised ability to efficiently explore and avoid obstacles in rmd mutants. We demonstrate that root circumnutation defects in rmd depend on brassinosteroid (BR) signaling, which is elevated in mutant roots. Suppressing BR signaling via pharmacological (BR inhibitor) or genetic (knockout of BR biosynthetic or signaling components) manipulation rescues root defects in rmd. We further reveal that mutations in MAPK6 suppress BR signaling and restore normal root circumnutation in rmd, which may be mediated by the interaction between MAPK6, MAPKK4 and BR signaling factor BIM2. Our study thus demonstrates that RMD and MAPK6 control root circumnutation by modulating BR signaling to facilitate early root growth.

IntroductionRemorins (REMs) are plant-specific membrane-associated proteins that play important roles in plant–pathogen interactions and environmental adaptations. Group I REMs are extensively involved in virus infection. However, little is known about the REM gene family in sugarcane (Saccharum spp. hyrid), the most important sugar and energy crop around world.MethodsComparative genomics were employed to analyze the REM gene family in Saccharum spontaneum. Transcriptomics or RT-qPCR were used to analyze their expression files in different development stages or tissues under different treatments. Yeast two hybrid, bimolecular fluorescence complementation and co-immunoprecipitation assays were applied to investigate the protein interaction.ResultsIn this study, 65 REMs were identified from Saccharum spontaneum genome and classified into six groups based on phylogenetic tree analysis. These REMs contain multiple cis-elements associated with growth, development, hormone and stress response. Expression profiling revealed that among different SsREMs with variable expression levels in different developmental stages or different tissues. A pair of alleles, ScREM1.5e-1/-2, were isolated from the sugarcane cultivar ROC22. ScREM1.5e-1/-2 were highly expressed in leaves, with the former expressed at significantly higher levels than the latter. Their expression was induced by treatment with H2O2, ABA, ethylene, brassinosteroid, SA or MeJA, and varied upon Sugarcane mosaic virus (SCMV) infection. ScREM1.5e-1 was localized to the plasma membrane (PM), while ScREM1.5e-2 was localized to the cytoplasm or nucleus. ScREM1.5e-1/-2 can self-interact and interact with each other, and interact with VPgs from SCMV, Sorghum mosaic virus, or Sugarcane streak mosaic virus. The interactions with VPgs relocated ScREM1.5e-1 from the PM to the cytoplasm.DiscussionThese results reveal the origin, distribution and evolution of the REM gene family in sugarcane and may shed light on engineering sugarcane resistance against sugarcane mosaic pathogens.

Alpine wetlands are an important source of methane (CH4) and play a key role in the global carbon cycle. Their CH4 emissions largely depend on microbial CH4 production and oxidation processes that involve external electron acceptors. Seasonal precipitation drives redox cycles of humic acids (HAs), iron oxide and sulfur species, which will in turn affect CH4 production and oxidation. To investigate the effects of electron acceptors on CH4 emissions, soil samples from a typical alpine wetland on the Tibetan Plateau were incubated with the addition of ferrihydrite (HFO), HAs, sodium sulfate (SO42-) or combinations (HAs-HFO, HAs-SO42- and HAs-HFO-SO42-). During long-term anaerobic incubation, CH4 concentrations showed similar trends, increasing rapidly from 0 to 60 days, decreasing from 60 to 240 days, and finally slowly increasing again after 240 days, in all treatments except the sterilised control. Thus, the incubation period was divided into the production, consumption and reproduction phases. The addition of HFO, HAs or HAs-containing electron acceptors promoted the rates of both production and consumption of CH4, increasing the production potential of CH4 by 65–100 % and the oxidation potential of CH4 by 58–115 %. On the other hand, SO42- inhibited the production and consumption of CH4, reducing the production potential by 35 % and the oxidation potential by 50 %. Electron acceptors such as HFO, HAs and SO42- play important roles in CH4 emissions. HAs are the dominant factor affecting CH4 emissions in alpine wetlands. From a broader ecological perspective, organic and inorganic electron acceptors play a key role in CH4 production and oxidation under anaerobic conditions, influencing CH4 emissions from alpine wetlands.

During photosynthesis, light energy is harvested by an antenna systems and delivered to the reaction centers (RCs) for charge separation and electron transfer (ET). The authors report cryo-EM structures of two forms of RC from the microaerophilic Chloracidobacterium thermophilum (CabRC), providing a structural basis for ET within the CabRC.

Stichopus ocellatus, known as eye-spotted sea cucumber, is a commercially important Stichopodidae holothuroid in Indo-Pacific region for its valuable nutrition and medicinal ingredients. However, because the taxonomic analyses based on morphological characters and molecular data within Aspidochirotida are limited, the deep-level evolutionary relationships of Aspidochirotida are still poorly understood. Here, for providing better insight of future evolutionary and taxonomic classification of Stichopodidae, we report the first complete mitogenome of S. ocellatus along with 37 annotated and characterized mitochondrial genes, and the phylogenetic analysis based on mitogenome data reveals sister relationship between S. ocellatus and S. monotuberculatus.

Abstract Formins are actin-binding proteins that are key to maintaining the actin cytoskeleton in cells. However, molecular mechanisms controlling the stability of formin proteins in plants remain unknown. Here, we have identified six rice SIAH-type E3 ligases, named RIP1-6 (RMD Interacting Protein 1–6) respectively, with ubiquitination enzyme activity in vitro. All six proteins can form homo- and hetero-dimers with themselves, and hetero-dimers with type II formin RMD/OsFH5. In vivo assays showed that RIP1-6 proteins localize in the cytoplasm with a punctate distribution, and all of them interact with RMD to change its native diffuse cytoplasmic localization to match that of RIP1-6. To our surprise, degradation experiments revealed that RIP1, RIP5, and RIP6 decrease rather than increase the degradation rate of RMD. Genetic analyses revealed redundancy between these six genes; either single or double mutants did not show any obvious phenotypes. However, the sextuple rip1-6 mutant displayed dwarf height, wrinkled seeds and wider leaves that were similar to the previously reported rmd mutant, and defective microfilaments and increased flag leaf angles that were not reported in rmd mutant. Collectively, our study provides insights into the mechanisms determining formin protein stability in plants.

Boron chloride in the chlorosilane is hard to remove and directly impacts the quality of polysilicon produced by improved Siemens method. Silicon dioxide functionalized with mannitol and citric acid successfully removed boron chloride in organic solution. The effects of immersion concentration and drying temperature were studied to attain the best adsorption performance. The sorption phenomenon was described well by pseudo-second-order kinetic model and Langmuir adsorption isotherm; particle diffusion model proved that the adsorption on the active adsorption site was the rate determining step, with the formation of boronic esters. Thermal stability and degradation kinetic of the adsorbents were investigated by thermogravimetric analysis. The characterization results of Fourier transform infrared spectroscopy, thermogravimetric analysis, X-ray energy spectrometry, and BET showed the silicon dioxide was successfully functionalized by oxygen-containing functional groups, leading to be a better and safer substitute to traditional boron-selective chelating resin.

In the present work, duplex stainless steels (DSSs) SAF2507 were friction stir processed with flowing cryogenic medium mixed with liquid nitrogen and industrial ethanol. Homogeneous ultrafine grained (UFG) dual-phase structure with ferrite (α) and austenite (γ) grains with average size of around 1 μm was obtained due to the significantly lower peak temperature and shorter high-temperature duration. The developed UFG dual-phase structure enabled a dramatic enhancement of yield strength by about 22 %, while maintaining a high elongation of 55 % owing to the excellent strain hardening capacity. The grain refinement and increased number of α/γ interfaces were dominantly responsible for the significantly improved YS, while the massive development of geometrically necessary dislocations around the deformation incompatible α/γ interfaces primarily contributed to improving the strain hardening capacity. As a result, the enhanced strength-ductility synergy was achieved by cryogenic friction stir processing. Also, the obtained UFG dual-phase structure helps with enhancing corrosion resistance. This work provides a new strategy for preparing uniform UFG DSSs with outstanding mechanical properties and anticorrosion.

Alumina-forming austenitic (AFA) steel is considered as a promising candidate used for advanced energy systems. Fusion welding of austenitic steels usually requires the introduction of a certain delta (δ) ferrite to avoid thermal cracking, but for the AFA steel, the presence of δ ferrite will greatly accelerate the precipitation of hard and brittle sigma (σ) phase at its target service temperature. In this work, for the AFA steel with a typical composition, we demonstrated a superior capability of friction stir welding (FSW) in avoiding the formation of δ and σ phases, and developing the favorable weld microstructures under various welding conditions. The microstructure evolution of AFA steel during FSW with various rotational speeds (300–700 rpm) was studied in detail. The resulting FSW joints all exhibit higher yield strength (YS) and ultimate tensile strength (UTS) than the base metal, especially at low rotational speed, while retaining reasonable ductility, despite decreasing with reducing rotational speed. The associated relationship between the microstructure and mechanical properties of the resulting FSW joints was well correlated. This work provides an effective method to obtain the fully-austenitic welded joints of AFA steel with excellent strength-ductility synergy.

Plant microbiota are of great importance for host nutrition and health. As a C4 plant species with a high carbon fixation capacity, sugarcane also associates with beneficial microbes, though mechanisms underlying sugarcane root-associated community development remain unclear. Here, we identify microbes that are specifically enriched around sugarcane roots and report results of functional testing of potentially beneficial microbes propagating with sugarcane plants. First, we analyzed recruitment of microbes through analysis of 16S rDNA enrichment in greenhouse cultured sugarcane seedlings growing in field soil. Then, plant-associated microbes were isolated and assayed for beneficial activity, first in greenhouse experiments, followed by field trials for selected microbial strains. The promising beneficial microbe SRB-109, which quickly colonized both roots and shoots of sugarcane plants, significantly promoted sugarcane growth in field trials, nitrogen and potassium acquisition increasing by 35.68 and 28.35%, respectively. Taken together, this report demonstrates successful identification and utilization of beneficial plant-associated microbes in sugarcane production. Further development might facilitate incorporation of such growth-promoting microbial applications in large-scale sugarcane production, which may not only increase yields but also reduce fertilizer costs and runoff.

Recently, 3D packaging has been regarded as an important technical means to continue Moore’s Law. However, excessive stacking will increase the longitudinal dimension, and one chip with high-density bondings packaging is still needed. Thus, it naturally places higher demand on thermal cycling reliability due to the decreased joint size to satisfy high-density packaging. In this work, the nano-Al2O3 (1 wt.%) modified Sn-1 wt.% Ag-0.5 wt.% Cu low-Ag solder was applied as a solder sample to evaluate the associated thermal cycling reliability. The investigated results revealed that the nano-Al2O3 modified solder did present enhanced thermal cycling reliability, as evidenced by the delayed microstructure coarsening and the inhibited atom inter-diffusion at interface caused by the adsorption of nano-Al2O3 on grain surfaces, and the resultant pinning effect. Worthy of note is that the potential of the newly developed nano-Al2O3 modified solder for high-density packaging applications (e.g., BGA, QFN, and CCGA) was evaluated based on the Finite Element Modeling.

Low- and ultra-low-grade thermal energy have significant recycling value for energy saving and carbon footprint reduction. Efficient thermal energy storage technology based on phase change materials (PCMs) will help improve heat recovery. This study aimed to develop a composite eutectic fatty acid of lauric acid (LA) and stearic acid (SA) binary system with expanded graphite (EG). The experimental measured eutectic temperature was 31.2 °C with an LA-to-SA mass ratio of 7:3. Afterwards, 1~15 wt.% EG was composited to the eutectic acid, and the thermophysical properties of the composite PCMs were measured by differential scanning calorimetry (DSC) and transient plane source (TPS) methods. The results demonstrated that the phase transition temperature and latent heat of the composite PCMs were stable when the content of EG was more than 5%, and the thermal conductivity and thermal diffusion coefficient of the composite PCMs (10–15 wt.%) increased by 2.4–2.6 and 3.2–3.7 times compared with the pure eutectic acid, respectively. On this basis, a finned-coil-type reservoir was prepared, and an experimental study of heat storage and heat release performance was carried out. The results showed that the heat storage and heat release effects of the heat reservoir were the best when the EG ratio was 10 wt.%. The heat storage time was reduced by 20.4%, 8.1%, and 6.2% compared with the other three EG ratios, respectively; meanwhile, the heat release time was reduced by 19.3%, 6.7%, and 5.3%, respectively.

Drought is the main abiotic stress that constrains sugarcane growth and production. To understand the molecular mechanisms that govern drought stress, we performed a comprehensive comparative analysis of physiological changes and transcriptome dynamics related to drought stress of highly drought-resistant (ROC22, cultivated genotype) and weakly drought-resistant (Badila, wild genotype) sugarcane, in a time-course experiment (0 h, 4 h, 8 h, 16 h and 32 h). Physiological examination reviewed that ROC22, which shows superior drought tolerance relative to Badila, has high performance photosynthesis and better anti-oxidation defenses under drought conditions. The time series dataset enabled the identification of important hubs and connections of gene expression networks. We identified 36,956 differentially expressed genes (DEGs) in response to drought stress. Of these, 15,871 DEGs were shared by the two genotypes, and 16,662 and 4423 DEGs were unique to ROC22 and Badila, respectively. Abscisic acid (ABA)-activated signaling pathway, response to water deprivation, response to salt stress and photosynthesis-related processes showed significant enrichment in the two genotypes under drought stress. At 4 h of drought stress, ROC22 had earlier stress signal transduction and specific up-regulation of the processes response to ABA, L-proline biosynthesis and MAPK signaling pathway–plant than Badila. WGCNA analysis used to compile a gene regulatory network for ROC22 and Badila leaves exposed to drought stress revealed important candidate genes, including several classical transcription factors: NAC87, JAMYB, bHLH84, NAC21/22, HOX24 and MYB102, which are related to some antioxidants and trehalose, and other genes. These results provide new insights and resources for future research and cultivation of drought-tolerant sugarcane varieties.