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Abstract Coreius guichenoti, mainly distributed in upstream regions of the Yangtze River China, is currently on the brink of extinction and listed as national secondary protected animal. In this study, we aimed to obtain the chromosome-level genome of C. guichenoti using PacBio and Hi-C techniques. According to the PacBio sequencing, C. guichenoti genome was successfully assembled to 1100.1 Mb size, with a Contig N50 size of 25.0 Mb, and containing 731.0 Mb of repeats. Hi-C sequencing data was utilized for chromosome assembly and 25 chromosome sequences were ultimately yielded, with a total length of 1076.8 Mb. Moreover, a total of 22,506 protein-coding genes were predicted with average intron length of 2293 bp. Evolutionary analysis and divergence time prediction revealed that C. guichenoti was closely related to C. heterodon and they phylogenetically diverged from common ancestor ~20.7 million years ago (Mya), following the separation of Cyprinidae at 28.3 Mya. In the future, the utilization of comparative genomics research is important in elucidating the molecular mechanisms of Ichthyophthirius disease and ensuring the conservation of biological resources.

To reveal the distribution characteristics of the non-uniform temperature field of structural steel under fire conditions, Q355B steel for grain storage was taken as the research object. A multi-channel temperature detection instrument was used to monitor the temperature distribution of Q355B test plate in real time under gas fire, and the distribution characteristics of the non-uniform temperature field of the steel were studied under different heat inputs. The results showed that the temperature changes within 600 mm from the flame point were significant, while the temperature changes beyond 600 mm were not sensitive. The peak temperature Tmax and the heating rate vr at the fire source points of each test plate increased linearly with the increase of heat input Q at the fire source. With the increase of distance d, the variation trend of the time tmax for each test plate to reach the peak temperature in the rolling direction, was the same. As d increased, tmax gradually increased and tended to stabilize. The average cooling rates vd1 and vd2 of each test plate decreased with the increase of d. The temperature distribution patterns of each test plate were the same. The Tmax-d curve of each test plate followed the Boltzmann function distribution, the Q-∆T followed a linear relationship, and the Q-d0 followed an exponential function relationship. By combining the three, a non-uniform distribution model of Tmax-Q temperature field under gas fire was obtained.

Abstract The rhizosphere microbiome is known to contain beneficial microorganisms that promote plant growth and increase tolerance to abiotic and biotic stresses. Understanding citrus microbiome diversity and the percentage of diversity that can be recovered in the laboratory is essential for developing innovative approaches to improve plant health and promote sustainable agricultural practices. However, information about the citrus root microbiome, especially in the context of exploring commercial citrus growing areas to identify beneficial plant growth-promoting rhizobacteria (PGPR), is scarce. Here, we present the microbiome data of healthy citrus trees sampled from geographical regions of São Paulo and Amazonas States, in Brazil. The resulting rhizosphere microbiome data comprise an average of 126,180 and 138,707 high-quality reads for the 16S rRNA V3–V4 and ITS1-5F regions, respectively. The taxonomic analysis of cultivated diversity revealed a total of 91 bacterial genera recovered in the laboratory. These data provide valuable information for understanding how the microbiome supports citrus plants in different environments and for developing new strategies to improve crop productivity by using PGPR.

Abstract This study investigated the effect of household air pollution on pregnant women with GDM, and assessed the modifying effect of a healthy lifestyle on this relationship. Household solid fuel exposure was defined as using solid fuels (coal, crop residue, and wood) for cooking and heating. Four individually modifiable lifestyle factors were assessed in early pregnancy: body mass index, diet, sleep, and vitamin D supplementation. Multifactorial logistic regression modeling was used to assess the relationship between household air pollution and GDM. A stratified analysis and additive interaction tested the effects of healthy lifestyle scores. After adjusting for potential confounders, we found that using solid fuels for heating was significantly associated with an increased risk of GDM (adjusted OR = 1.60, 95% CI 1.18–2.18). GDM risk showed a decreasing trend in the medium versus the high score group when compared to the low score group, with a consistent trend regardless of household fuel type used (adjusted OR = 0.39, 95% CI 0.27–0.57) (adjusted OR = 0.12, 95% CI 0.05–0.28), respectively. Importantly, when the healthy lifestyle score increased, exposure to household air pollution was no longer associated with a higher GDM risk. There was a negative additive interaction between exposure to household solid fuels exposure and a healthy lifestyle (FERI: −5.10 [−16.48, −2.04]; AP: −1.29 [−2.80, −0.39]; SI: −0.37 [−0.20, −0.67]). We determined that exposure to household air pollution may be an important GDM risk factor. In addition, A healthy lifestyle may have a protective effect on women with GDM exposed to indoor fuel air pollution.

The Yangtze River is the mother river of China. To promote the aquatic ecosystem protection of the great river, the Project of Yangtze Fisheries Resources and Environment Investigation (2017–2021) supported by the Ministry of Agriculture and Rural Affairs, P. R. China carried out by 24 institutes and universities that located in the Yangtze River basin surveys the status of (1) fish species composition and spatial distribution, (2) current fish abundance, (3) endangered fishes, (4) Yangtze finless porpoise, (5) aquatic eco-environments, (6) water-level fluctuation areas, (7) capture fisheries and recreational fisheries of the Yangtze River mainstream and 10 of its main tributaries, including Yalong River, Heng River, Min River (including Dadu River), Chishui River, Tuo River, Jialing River, Wu River, Han River, Dongting Lake and Poyang Lake. The results showed that there were 443 fish species (belonging to 163 genus, 37 families, and 18 orders) before 2017, but only 323 fish species (including 15 new recorded exotic species) were recorded in the project of 2017–2021. Among them, Cyprinus carpio, Carassius auratus, Hypophthalmichthys molitrix, Pelteobagrus fulvidraco, Coilia brachygnathus, Silurus asotus, Saurogobio dabryi, Ctenopharyngodon idellus, Pelteobagrus nitidus, Hemiculter leucisculus, Siniperca chuatsi, Coreius heterodon, Culter alburnus, Parabramis pekinensis, and Aristichthys nobilis were the dominant species across the whole Yangtze River system. It is estimated that there were 886 million individuals weighing 124.8 million kg, merely equivalent to 27.3% of the resources in 1950s, 30.9% of the resources in 1960s, or 58.7% of the resources in 1980s. In the new list of protected fishes that recorded in the Yangtze River system, only 15 of 29 were collected in this project of 2017–2021. Psephurus gladius has been affirmed to be Extinct by International Union for Conservation of Nature (IUCN). The wild individuals of Tenualosa reevesii and Luciobrama macrocephalus have disappeared for many years and maybe have been extinct already. Acipenser dabryanus has been affirmed to be Extinct in the Wild by IUCN. The natural propagations of A. sinensis, Myxocyprinus asiaticus and Trachidermus fasciatus have been interrupted for many years. The populations of Yangtze finless porpoise in the Yangtze River mainstream, Dongting Lake and Poyang Lake have steadily rising sizes and expanding distributions in 2017–2021. Parts of them migrate from one region to another with the seasons, which would result in the fluctuation of Yangtze finless porpoise population within some regions. The conventional indicators of water quality in the Yangtze River system were good and conformed to the water quality criteria of fishery in 2017–2021. In the last 40 years, the maximum surface water area in the Yangtze River basin extended to approximately 63,360 km2, the minimum surface water area covered approximately 26,396 km2, and the seasonal water-level fluctuation areas occupied approximately 36,964 km2. Compared with 1984–2000 period, the 2001–2020 period witnessed an overall decreasing trend in the frequency of surface water occurrence within about 25,869 km2 of aquatic areas. From 1984 to 2000 period to 2001–2020 period, permanent surface water has decreased by nearly 8,750 km2. In 2017, the fishermen were mainly 40–60 years old and their educational levels were mainly lower than junior high school. In 2017, most anglers were older than 40 and used hand rod and/or sea rod. Their average catch of each time was mainly less than 1 kg. Results suggested that the fishing ban in key waters of the Yangtze River basin is not only an ecological project of aquatic ecosystem conservation, but also a livelihood project for the fisherman to embrace industrial transformation and improve their living conditions. After the implementation of the fishing ban, the fisheries resources would gradually recover, and the Yangtze finless porpoise population size would also see a steady increase. However, the endangered species would remain threatened for a long time. The degraded waterbodies and water-level fluctuation areas would be the key restrictive factors for future aquatic ecosystem recovery in the Yangtze River basin. Since this survey was carried out before the fishing ban, the current results could provide a baseline for future evaluation of the effect of the Yangtze River fishing ban.

Abstract Flexible strain monitoring of hand and joint muscle movement is recognized as an effective method for the diagnosis and rehabilitation of neurological diseases such as stroke and Parkinson's disease. However, balancing high sensitivity and large strain, improving wearing comfort, and solving the separation of diagnosis and treatment are important challenges for further building tele‐healthcare systems. Herein, a hydrogel‐based optical waveguide stretchable (HOWS) sensor is proposed in this paper. A double network structure is adopted to allow the HOWS sensor to exhibit high stretchability of the tensile strain up to 600% and sensitivity of 0.685 mV %−1. Additionally, the flexible smart bionic fabric embedding the HOWS sensor, produced through the warp and weft knitting, significantly enhances wearing comfort. A small circuit board is prepared to enable wireless signal transmission of the designed sensor, thereby improving the daily portability. A speech recognition and human‐machine interaction system, based on sensor signal acquisition, is constructed, and the convolutional neural network algorithm is integrated for disease assessment. By integrating sensing, wireless transmission, and artificial intelligence (AI), a smart tele‐healthcare system based on HOWS sensors is demonstrated to hold great potential for early warning and rehabilitation monitoring of neurological diseases.

In this article, a fast two-grid mixed finite element (T-GMFE) algorithm based on a time second-order discrete scheme with parameter θ is considered to numerically solve a class of two-dimensional nonlinear fractional pseudo-hyperbolic wave models. The weighted and shifted Grünwald difference (WSGD) formula is used to approximate the fractional time derivative at time tn−θ, and the spatial direction is approximated by a two-grid H1-Galerkin MFE method. The error estimates in both L2 and H1-norm for the fully discrete T-GMFE system are proved. Further, a modified T-GMFE scheme is proposed and the optimal error results are provided. Finally, computing results show the presented T-GMFE method can save computing time and improve the computational efficiency.

Diffusion magnetic resonance imaging (MRI) has been utilized to probe the renal microstructures but investigating the three-dimensional (3D) tubular network still presents significant challenges due to the complicated architecture of kidney. This study aims to assess whether high angular resolution diffusion imaging (HARDI) could improve the reconstruction of 3D tubular architectures. Kidneys from both mice and rats were imaged using 3D diffusion-weighted pulse sequences at 9.4 T. Five healthy mouse kidneys were scanned at an isotropic spatial resolution of 40 μm, with a b value of 1500 s/mm2 across 46 diffusion encoding directions. The study employed diffusion tensor imaging (DTI) and generalized Q-sampling imaging (GQI) to examine the tubular orientation distributions and tractography, validated by conventional histology. Fractional anisotropy (FA) and mean diffusivity (MD) were quantified and compared among the inner medullar (IM), outer medullar (OM), and cortex (CO) at different angular resolutions. FA values, estimated with 6 diffusion-weighted images (DWIs), were significantly overestimated by 49.9% (p

Many studies have indicated that individual exposure to phthalates (PAEs) or polycyclic aromatic hydrocarbons (PAHs) affects pregnancy outcomes. However, combined exposure to PAEs and PAHs presents a more realistic situation, and research on the combined effects of PAEs and PAHs on gestational age and newborn size is still limited. This study aimed to assess the effects of combined exposure to PAEs and PAHs on neonatal gestational age and birth size. Levels of 9 PAE and 10 PAH metabolites were measured from the urine samples of 1030 women during early pregnancy from the Zunyi Birth Cohort in China. Various statistical models, including linear regression, restricted cubic spline, Bayesian kernel machine regression, and quantile g-computation, were used to study the individual effects, dose–response relationships, and combined effects, respectively. The results of this prospective study revealed that each ten-fold increase in the concentration of monoethyl phthalate (MEP), 2-hydroxynaphthalene (2-OHNap), 2-hydroxyphenanthrene (2-OHPhe), and 1-hydroxypyrene (1-OHPyr) decreased gestational age by 1.033 days (95 % CI: −1.748, −0.319), 0.647 days (95 % CI: −1.076, −0.219), 0.845 days (95 % CI: −1.430, −0.260), and 0.888 days (95 % CI: −1.398, −0.378), respectively. Moreover, when the concentrations of MEP, 2-OHNap, 2-OHPhe, and 1-OHPyr exceeded 0.528, 0.039, 0.012, and 0.002 µg/g Cr, respectively, gestational age decreased in a dose–response manner. Upon analyzing the selected PAE and PAH metabolites as a mixture, we found that they were significantly negatively associated with gestational age, birth weight, and the ponderal index, with 1-OHPyr being the most important contributor. These findings highlight the adverse effects of single and combined exposure to PAEs and PAHs on gestational age. Therefore, future longitudinal cohort studies with larger sample sizes should be conducted across different geographic regions and ethnic groups to confirm the impact of combined exposure to PAEs and PAHs on birth outcomes.

Abstract Accurate prediction of protein‐ligand binding affinities is an essential challenge in structure‐based drug design. Despite recent advances in data‐driven methods for affinity prediction, their accuracy is still limited, partially because they only take advantage of static crystal structures while the actual binding affinities are generally determined by the thermodynamic ensembles between proteins and ligands. One effective way to approximate such a thermodynamic ensemble is to use molecular dynamics (MD) simulation. Here, an MD dataset containing 3,218 different protein‐ligand complexes is curated, and Dynaformer, a graph‐based deep learning model is further developed to predict the binding affinities by learning the geometric characteristics of the protein‐ligand interactions from the MD trajectories. In silico experiments demonstrated that the model exhibits state‐of‐the‐art scoring and ranking power on the CASF‐2016 benchmark dataset, outperforming the methods hitherto reported. Moreover, in a virtual screening on heat shock protein 90 (HSP90) using Dynaformer, 20 candidates are identified and their binding affinities are further experimentally validated. Dynaformer displayed promising results in virtual drug screening, revealing 12 hit compounds (two are in the submicromolar range), including several novel scaffolds. Overall, these results demonstrated that the approach offer a promising avenue for accelerating the early drug discovery process.

Rhododendron is famous for its high ornamental value. However, the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved. In addition, the origin of key morphological characters with high horticulture value need to be explored. Both problems largely hinder utilization of germplasm resources. Most studies attempted to disentangle the phylogeny of Rhododendron, but only used a few genomic markers and lacked large-scale sampling, resulting in low clade support and contradictory phylogenetic signals. Here, we used restriction-site associated DNA sequencing (RAD-seq) data and morphological traits for 144 species of Rhododendron, representing all subgenera and most sections and subsections of this species-rich genus, to decipher its intricate evolutionary history and reconstruct ancestral state. Our results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq data. Both optimal phylogenetic tree and split tree recovered five lineages among Rhododendron. Subg. Therorhodion (clade I) formed the basal lineage. Subg. Tsutsusi and Azaleastrum formed clade II and had sister relationships. Clade III included all scaly rhododendron species. Subg. Pentanthera (clade IV) formed a sister group to Subg. Hymenanthes (clade V). The results of ancestral state reconstruction showed that Rhododendron ancestor was a deciduous woody plant with terminal inflorescence, ten stamens, leaf blade without scales and broadly funnelform corolla with pink or purple color. This study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq data. It also provides an example to resolve discordant signals in phylogenetic trees and demonstrates the application feasibility of RAD-seq with large amounts of missing data in deciphering intricate evolutionary relationships. Additionally, the reconstructed ancestral state of six important characters provides insights into the innovation of key characters in Rhododendron.

Abstract Background Citrus is a major fruit crop, and RNA-sequencing (RNA-seq) data can be utilized to investigate its gene functions, heredity, evolution, development, and the detection of genes linked to essential traits or resistance to pathogens. However, it is challenging to use the public RNA-seq datasets for researchers without bioinformatics training, and expertise. Results OrangeExpDB is a web-based database that integrates transcriptome data of various Citrus spp., including C. limon (L.) Burm., C. maxima (Burm.) Merr., C. reticulata Blanco, C. sinensis (L.) Osbeck, and Poncirus trifoliata (L.) Raf., downloaded from the NCBI SRA database. It features a blast tool for browsing and searching, enabling quick download of expression matrices for different transcriptome samples. Expression of genes of interest can be easily generated by searching gene IDs or sequence similarity. Expression data in text format can be downloaded and presented as a heatmap, with additional sample information provided at the bottom of the webpage. Conclusions Researchers can utilize OrangeExpDB to facilitate functional genomic analysis and identify key candidate genes, leveraging publicly available citrus RNA-seq datasets. OrangeExpDB can be accessed at http://www.orangeexpdb.com/ .

In order to reveal the non-uniform distribution of grain size in thick direction for engineering heavy plate, microstructure of 40 mm-thick Q345 steel was observed and measured under different short-term high temperature environments formed by fire. Moreover, the influence of the short-term high temperature environment was revealed on the distribution of ferrite grain size in the Q345 steel. Under different fire service environments, there was a log-normal distribution relationship between the distribution parameter Nf (number of ferrite grains) and df (average grain diameter), as well as ρAf (area fraction density) and df, at different positions along the thickness direction. However, the statistical results are greatly affected by the length of the statistical interval. When df is about 4 to 6 times the length of the statistical interval, the statistical accuracy is higher. By using nonlinear fitting method, multiple non-uniform distribution empirical models including Nf-df empirical formulas and ρAf-df empirical formulas were established at different positions along thick direction under various fire environments. Furthermore, the interrelationships between fire temperature T and Nf , T and ρAf , fire duration t and Nf , t and ρAf were revealed, respectively.

Abstract Background Increasing evidence indicates that four and a half LIM domains 2 (FHL2) plays a crucial role in the progression of various cancers. However, the biological functions and molecular mechanism of FHL2 in lung adenocarcinoma (LUAD) remain unclear. Methods We evaluated the prognostic value of FHL2 in LUAD using public datasets and further confirmed its prognostic value with our clinical data. The biological functions of FHL2 in LUAD were evaluated by in vitro and in vivo experiments. Pathway analysis and rescue experiments were subsequently performed to explore the molecular mechanism by which FHL2 promoted the progression of LUAD. Results FHL2 was upregulated in LUAD tissues compared to adjacent normal lung tissues, and FHL2 overexpression was correlated with unfavorable outcomes in patients with LUAD. FHL2 knockdown significantly suppressed the proliferation, migration and invasion of LUAD cells, while FHL2 overexpression had the opposite effect. Mechanistically, FHL2 upregulated the PI3K/AKT/mTOR pathway and subsequently inhibited autophagy in LUAD cells. The effects FHL2 on the proliferation, migration and invasion of LUAD cells are dependent on the inhibition of autophagy, as of induction autophagy attenuated the aggressive phenotype induced by FHL2 overexpression. Conclusions FHL2 promotes the progression of LUAD by activating the PI3K/AKT/mTOR pathway and subsequently inhibiting autophagy, which can be exploited as a potential therapeutic target for LUAD.

The biosynthesis of bioactive secondary metabolites, specifically antibiotics, is of great scientific and economic importance. The control of antibiotic production typically involves different processes and molecular mechanism. Despite numerous efforts to improve antibiotic yields, joint engineering strategies for combining genetic manipulation with fermentation optimization remain finite. Lincomycin A (Lin-A), a lincosamide antibiotic, is industrially fermented by Streptomyces lincolnensis. Herein, the leucine-responsive regulatory protein (Lrp)-type regulator SLCG_4846 was confirmed to directly inhibit the lincomycin biosynthesis, whereas indirectly controlled the transcription of SLCG_2919, the first reported repressor in S. lincolnensis. Inactivation of SLCG_4846 in the high-yield S. lincolnensis LA219X (LA219XΔ4846) increases the Lin-A production and deletion of SLCG_2919 in LA219XΔ4846 exhibits superimposed yield increment. Given the effect of the double deletion on cellular primary metabolism of S. lincolnensis, Plackett-Burman design, steepest ascent and response surface methodologies were utilized and employed to optimize the seed medium of this double mutant in shake flask, and Lin-A yield using optimal seed medium was significantly increased over the control. Above strategies were performed in a 15-L fermenter. The maximal yield of Lin-A in LA219XΔ4846-2919 reached 6.56 g/L at 216 h, 55.1 % higher than that in LA219X at the parental cultivation (4.23 g/L). This study not only showcases the potential of this strategy to boost lincomycin production, but also could empower the development of high-performance actinomycetes for other antibiotics.

IntroductionCitrus canker, caused by Xanthomonas citri subsp. citri (Xcc), is a devastating disease worldwide. Previously, we successfully generated canker-resistant Citrus sinensis cv. Hamlin lines in the T0 generation. This was achieved through the transformation of embryogenic protoplasts using the ribonucleoprotein (RNP) containing Cas12a and one crRNA to edit the canker susceptibility gene, CsLOB1, which led to small indels.MethodsHere, we transformed embryogenic protoplasts of Hamlin with RNP containing Cas12a and three crRNAs.ResultsAmong the 10 transgene-free genome-edited lines, long deletions were obtained in five lines. Additionally, inversions were observed in three of the five edited lines with long deletions, but not in any edited lines with short indel mutations, suggesting long deletions maybe required for inversions. Biallelic mutations were observed for each of the three target sites in four of the 10 edited lines when three crRNAs were used, demonstrating that transformation of embryogenic citrus protoplasts with Cas12a and three crRNAs RNP can be very efficient for multiplex editing. Our analysis revealed the absence of off-target mutations in the edited lines. These cslob1 mutant lines were canker- resistant and no canker symptoms were observed after inoculation with Xcc and Xcc growth was significantly reduced in the cslob1 mutant lines compared to the wild type plants.DiscussionTaken together, RNP (Cas12a and three crRNAs) transformation of embryogenic protoplasts of citrus provides a promising solution for transgene-free multiplex genome editing with high efficiency and for deletion of long fragments.

Brain development is a highly complex process regulated by numerous genes at the molecular and cellular levels. Brain tissue exhibits serial microstructural changes during the development process. High-resolution diffusion magnetic resonance imaging (dMRI) affords a unique opportunity to probe these changes in the developing brain non-destructively. In this study, we acquired multi-shell dMRI datasets at 32 µm isotropic resolution to investigate the tissue microstructure alterations, which we believe to be the highest spatial resolution dMRI datasets obtained for postnatal mouse brains. We adapted the Allen Developing Mouse Brain Atlas (ADMBA) to integrate quantitative MRI metrics and spatial transcriptomics. Diffusion tensor imaging (DTI), diffusion kurtosis imaging (DKI), and neurite orientation dispersion and density imaging (NODDI) metrics were used to quantify brain development at different postnatal days. We demonstrated that the differential evolutions of fiber orientation distributions contribute to the distinct development patterns in white matter (WM) and gray matter (GM). Furthermore, the genes enriched in the nervous system that regulate brain structure and function were expressed in spatial correlation with age-matched dMRI. This study is the first one providing high-resolution dMRI, including DTI, DKI, and NODDI models, to trace mouse brain microstructural changes in WM and GM during postnatal development. This study also highlighted the genotype-phenotype correlation of spatial transcriptomics and dMRI, which may improve our understanding of brain microstructure changes at the molecular level.

IntroductionCitrus is one of the most important fruit crops worldwide, and the root-associated microbiota can have a profound impact on tree health and growth.MethodsIn a collaborative effort, the International Citrus Microbiome Consortium investigated the global citrus root microbiota with samples collected from nine citrus-producing countries across six continents. We analyzed 16S rDNA and ITS2 amplicon sequencing data to identify predominant prokaryotic and fungal taxa in citrus root samples. Comparative analyses were conducted between root-associated microbial communities and those from the corresponding rhizosphere and bulk soil samples. Additionally, genotype-based group-wise comparisons were performed to assess the impact of citrus genotype on root microbiota composition.ResultsTen predominant prokaryotic phyla, containing nine bacterial phyla including Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes and one archaeal phylum (Thaumarchaeota), and multiple fungal phyla including Ascomycota and Basidiomycota were identified in the citrus root samples. Compared with the microbial communities from the corresponding rhizosphere and bulk soil samples from the same trees, the prokaryotic and fungal communities in the roots exhibited lower diversity and complexity but greater modularity compared to those in the rhizosphere. In total, 30 root-enriched and 150 root-depleted genera in bacterial community were identified, whereas 21 fungal genera were enriched, and 147 fungal genera were depleted in the root niche compared with the rhizosphere. The citrus genotype significantly affected the root prokaryotic and fungal communities. In addition, we have identified the core root prokaryotic genera comprising Acidibacter, Allorhizobium, Bradyrhizobium, Chitinophaga, Cupriavidus, Devosia, Dongia, Niastella, Pseudomonas, Sphingobium, Steroidobacter and Streptomyces, and the core fungal genera including Acrocalymma, Cladosporium, Fusarium, Gibberella, Mortierella, Neocosmospora and Volutella. The potential functions of these core genera of root microbiota were predicted.ConclusionOverall, this study provides new insights into the assembly of microbial communities and identifies core members of citrus root microbiota across a wide geographic range. The findings offer valuable information for manipulating root microbiota to enhance plant growth and health.

Colorectal cancer (CRC) is one of the most common malignant tumors of the digestive tract. In recent years, the age at which CRC is diagnosed has been trending younger on a global scale. Obesity, as a worldwide epidemic, is on the rise in most countries due to changes in dietary habits and lifestyles. Concurrently, with increased screening efforts and growing public awareness of health, the incidence of CRC in older adults is gradually declining, while the incidence in younger and middle-aged individuals is steadily increasing. This seems to indicate a strong association between overweight and obesity and a younger age of colorectal cancer diagnosis. Currently, with advancements in research on the relationship between early life (childhood and adolescence) body weight and CRC, new insights have been gained regarding the role of high BMI (overweight and obesity) in the occurrence and development of CRC, as well as its impact at different early life stages. Adolescence appears to be a particularly critical period. Therefore, this review will summarize the relationship between early life high BMI and CRC, aiming to provide a reference for clinical and basic research as well as CRC prevention. Significance This study on the relationship between early life high BMI and the development of CRC reveals the role of high BMI during childhood and adolescence in the occurrence and progression of CRC. It suggests the importance of restoring normal weight or reducing weight in individuals with high BMI early in life for the prevention of colorectal cancer.

BackgroundHepatocellular carcinoma (HCC) is the most common type of liver cancer. Small extracellular vesicles (sEVs) are bilayer lipid membrane vesicles containing RNA that exhibit promising diagnostic and prognostic potential as cancer biomarkers.AimsTo establish a miRNA panel from peripheral blood for use as a noninvasive biomarker for the diagnosis of HCC.MethodssEVs obtained from plasma were profiled using high-throughput sequencing. The identified differential miRNA expression patterns were subsequently validated using quantitative real-time polymerase chain reaction analysis.ResultsThe random forest method identified ten distinct miRNAs distinguishing HCC plasma from non-HCC plasma. During validation, miR-140-3p (p = 0.0001) and miR-3200-3p (p = 0.0017) exhibited significant downregulation. Enrichment analysis uncovered a notable correlation between the target genes of these miRNAs and cancer development. Utilizing logistic regression, we developed a diagnostic model incorporating these validated miRNAs. Receiver operating characteristic (ROC) curve analysis revealed an area under the curve (AUC) of 0.951, with a sensitivity of 90.1% and specificity of 87.8%.ConclusionThese aberrantly expressed miRNAs delivered by sEVs potentially contribute to HCC pathology and may serve as diagnostic biomarkers for HCC.

Poplar line NL895 can potentially become a model plant for poplar study as it is a widely cultivated elite line. However, the lack of genome resources hindered the use of NL895 as the major plant material in poplar. In this study, we provided a high-quality genome assembly for poplar line NL895 with PacBio single molecule real-time (SMRT) sequencing and High-throughput chromosome conformation capture (Hi-C) technology. The raw assembly of NL895 for the diploid genome included 606 contigs with a total size of ~815 Mb, and the monoploid genome included 246 contigs with a total size of ~412 Mb. The haplotype-resolved chromosomes in the diploid genomes were also generated. All the monoploid, diploid, and haplotype-resolved genomes showed more than 97% completeness and they can largely improve the mapping efficiency in RNA-Seq analysis. By comprehensively comparing the two haplotype genomes we found the heterozygosity of NL895 is much higher than other poplar lines. We also found that NL895 harbors more genomic variants and more gene diversity. The haplotype-specific genes showed higher variable gene expression patterns. These characters would be attributed to the high heterosis of poplar line NL895. The allele-specific expression (ASE) was also investigated and lots of alleles showed biased expressions in different tissues or environmental conditions. Taken together, the genome sequence for NL895 is a valuable tree genomic resource and it would greatly facilitate studies in poplar.

Introduction: Sea-island cotton (Gossypium barbadense, Gb) is one of the major sources of high-grade natural fiber. Besides the common annual Gb cotton, perennial Gb cotton is also cultivated, but studies on perennial Gb cotton are rare. Objectives: We aimed to make a systematic analysis of perennial sea-island cotton and lay a foundation for its utilization in breeding, and try to identify the representative structural variations (SVs) in sea-island cotton, and to reveal the population differentiation and adaptive improvement of sea-island cotton. Methods: Through genome assembly of one perennial Gb cotton accession (named Gb_M210936) and comparative genome analysis, variations during Gb cotton domestication were identified by comparing Gb_M210936 with annual Gb accession 3–79 and with wild allotetraploid cotton G. darwinii. Six perennial Gb accessions combining with the resequenced 1,129 cotton accessions were used to conduct population and genetic analysis. Large haplotype blocks (haploblocks), generated from interspecific introgressions and intraspecific inversions, were identified and were used to analyze their effects on population differentiation and agronomic traits of sea-island cotton. Results: One reference genome of perennial sea-island cotton was assembled. Representative SVs in sea-island cotton were identified, and 31 SVs were found to be associated with agronomic traits. Perennial Gb cotton had a closer kinship with the wild-to-landrace continuum Gb cotton from south America where Gb cotton is originally domesticated. Haploblocks were associated with agronomic traits improvement of sea-island cotton, promoted sea-island cotton differentiation into three subgroups, were suffered from breeding selection, and may drive Gb cotton to be adapted to central Asian. Conclusion: Our study made up the lack of perennial Gb cotton genome, and clarified that exotic introgressions improved the traits of sea-island cotton, promoted the population differentiation, and drove sea-island cotton adaptive to central Asia, which will provide new insights for the genetic breeding improvement of sea-island cottons.

Grapevine berry inner necrosis virus (GINV) and grapevine Pinot gris virus (GPGV) are prevalent viral diseases affecting viticulture, posing significant threats in grape-producing regions of China. Previous studies have emphasized the harmful effects of grape viruses on the grape industry all over the world. However, few reports have focused specifically on GINV. In wild grapevines, GINV infection frequently leads to grapevine fanleaf degeneration disease (GFDD). GINV often co-occurs with other grape viruses, exacerbating its harmful effects on the grapevine industry in China. In this study, we collected grapevine samples from Taizhou city, Jiangsu Province, where GINV infection was confirmed. Based on the GINV coat protein (CP) gene, we developed a high-throughput and high-sensitivity direct antigen-coated ELISA and Dot blot assay for field diagnosis of GINV CP in grape samples. The CP gene was cloned from GINV-infected grape samples, and the GINV CP was expressed using the pET30(a) vector. Specific polyclonal antiserum CPGINV was generated by immunizing rabbits with the purified protein, and its sensitivity was determined to be satisfactory. Leveraging the high accuracy and sensitivity of the CPGINV antiserum, we developed a rapid, precise, and scalable diagnostic method for GINV in the grapevine industry. The established ELISA and Dot blot assays successfully detected GINV-infected grapevine samples. The occurrence of GINV is relatively common in China, which poses a risk of transmission and threatens the healthy development of the grape industry. Therefore, this study prepared CPGINV antiserum and established an efficient, rapid, sensitive, accurate, and high-throughput diagnostic method, providing a foundational approach for the prevention and control of vitis viral diseases.

While many neural networks have been proposed for hyperspectral image classification, current backbones cannot achieve accurate results due to the insufficient representation by scalar features and always cause a cumbersome calculation burden. To solve the problem, we propose the capsule attention network (CAN), which combines an activity vector with an attention mechanism to improve HSI classification. In particular, we consider two attention mechanisms to improve the effectiveness of the activity vectors. First, an attention-based feature extraction (AFE) module is proposed to preprocess the spectral-spatial features of HSI data, which effectively mines useful information before the generation of the activity vectors. Second, we propose a self-weighted mechanism (SWM) to distinguish the importance of different capsule convolutions, which enhances the representation of the primary activity vectors. Experiments on four well-known HSI datasets have shown our CAN surpasses state-of-the-art (SOTA) methods on three widely used metrics with a much lower computational burden.

One of the crucial factors influencing the growth and viability of larvae and juveniles is their opening diets. The objective of this study was to identify suitable initial feed options for M. macropterus larvae and juveniles. A total of 1200 newly hatched M. macropterus with an average weight of 18.3 mg and an average length of 11.58 mm were selected and randomly divided into four groups. The fish were fed with different opening diets, including rotifer, Artemia nauplii, Tubifex, and micro-diet from six days after hatching (dahs), respectively. Growth indices and activities of digestive enzymes were assessed at 10, 15, 20, 25, 30, 35, and 40 dahs. Histological examination of the structure of the digestive tract was performed at 40 dahs, while survival rates were also documented. The results demonstrated that different diets had no effect on the survival rate of larvae and juveniles of M. macropterus. The growth performance indices were ranked as follows: Tubifex group > Artemia nauplii group > micro-diet group > rotifer group. Remarkably, the Tubifex group exhibited superior growth performance, which was also reflected in the structure of the digestive tract and digestive enzyme activity. Therefore, it is recommended to include Tubifex in the diet of M. macropterus larvae and juvenile during the standardized farming process.

Although plant genotypes are known to be a determinant of microbiome composition, the genetic mechanisms underlying how genotypes affect the microbiome are poorly understood. Citrus is an important, perennial fruit crop that normally contains scion grafted on the rootstock. Here, we investigated the genetic traits underlying the citrus microbiome. We sequenced the metagenome of leaf, root, and rhizosphere soil samples and the genome of corresponding citrus genotypes, which included 66 unique rootstock–scion combinations (56 scion genotypes and 9 rootstock genotypes) from one location using deep shotgun sequencing. Using a genome-wide association study (GWAS) analysis, we identified significant associations between citrus genes and a subset of genera and functional traits of the microbiome. Intriguingly, we found that bacterial secretion systems and mobility-related genes were present in single-nucleotide polymorphism-associated microbial functional traits of leaf and root microbiomes but not in the rhizosphere microbiome, indicating that they are important factors for bacteria to colonize inside or on leaf and root tissues but less so in the rhizosphere. We also discovered that chemotaxis and flagella genes play critical roles for bacteria colonizing leaf tissues but not in root tissues and the rhizosphere. Microbiome-associated host genes were mainly involved in plant immunity, transporters, hormones, cell walls, and the metabolism of carbohydrates, amino acids, and nitrogen. We identified genetic determinants that are associated with the abundance of Bacillus, Bradyrhizobium, Burkholderia, and Cellvibrio, genera that are known to comprise many beneficial bacteria for citrus. This study unraveled the genetic traits underneath the mutual selection of citrus and microbes via GWAS analyses. This study provides useful information that aids the utilization of genotypes and key members of a healthy microbiota for microbiome engineering as well as the editing of specific genes to improve host microbiota. [Graphic: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Abstract The bacterium Candidatus Liberibacter asiaticus (CLas) causes citrus Huanglongbing disease. Our understanding of the pathogenicity and biology of this microorganism remains limited because CLas has not yet been cultivated in artificial media. Its genome is relatively small and encodes approximately 1136 proteins, of which 415 have unknown functions. Here, we use a high-throughput yeast-two-hybrid (Y2H) screen to identify interactions between CLas proteins, thus providing insights into their potential functions. We identify 4245 interactions between 542 proteins, after screening 916 bait and 936 prey proteins. The false positive rate of the Y2H assay is estimated to be 2.9%. Pull-down assays for nine protein-protein interactions (PPIs) likely involved in flagellar function support the robustness of the Y2H results. The average number of PPIs per node in the CLas interactome is 15.6, which is higher than the numbers previously reported for interactomes of free-living bacteria, suggesting that CLas genome reduction has been accompanied by increased protein multi-functionality. We propose potential functions for 171 uncharacterized proteins, based on the PPI results, guilt-by-association analyses, and comparison with data from other bacterial species. We identify 40 hub-node proteins, including quinone oxidoreductase and LysR, which are known to protect other bacteria against oxidative stress and might be important for CLas survival in the phloem. We expect our PPI database to facilitate research on CLas biology and pathogenicity mechanisms.

The term plant growth-promoting rhizobacteria (PGPR) refers to a root-associated bacteria that possesses several benefits for soil and the plant. The increasing demand for sustainable food production necessitates a shift towards agricultural practices that mitigate adverse environmental impacts. Excessive use of chemical fertilizers and pesticides has raised concerns, prompting a surge of interest in harnessing the potential of beneficial soil microorganisms, particularly plant growth-promoting rhizobacteria. This study explores the impact of soil inoculation with PGPR treatments on grapefruit seedlings, including a commercial strain of Bacillus velezensis, a fresh inoculum of Bacillus amyloliquefaciens, a mixture of three selected citrus endophytic Bacillus spp. isolates, inorganic fertilizers, and combinations thereof. The aim was to test their ability to enhance growth and nutrient uptake reducing the input of chemical fertilization. Results indicated that the combination of Bacillus velezensis and inorganic fertilization significantly improved soil nutrient availability and enhanced plant growth, surpassing both negative (water) and positive (inorganic fertilization) controls. Shoot and root system biomass showed significant increases from Bacillus velezensis plus inorganic fertilization compared to other treatments. These findings provide insights into management methods that can reduce chemical inputs while promoting plant productivity. The demonstrated benefits of PGPR on grapefruit seedlings highlight a promising approach for future research and applications in sustainable citrus cultivation.

Nonaqueous Li metal batteries (LMBs) and aqueous Zn metal batteries (ZMBs) are promising next-generation secondary batteries owing to their high energy density. Selecting an appropriate electrolyte is critical for addressing the safety issues nonaqueous and aqueous metal batteries can encounter. Ionic liquids (ILs) have been widely used in secondary metal batteries because they are non-flammable, present good thermal stability, and have wide electrochemical windows. This review highlights the research progress on IL-based electrolytes for stable Li/Zn metal anodes. We focus particularly on these electrolytes' electrochemistry and functionalities at the electrolyte/anode interface for inhibiting dendrite growth, preventing side reactions, and enhancing electrochemical performance. It is expected that this review will shed some light on the development of ILs for next-generation metal batteries.

Citrus canker disease affects citrus production. This disease is caused by Xanthomonas citri subsp. citri (Xcc). Previous studies confirmed that during Xcc infection, PthA4, a transcriptional activator like effector (TALE), is translocated from the pathogen to host plant cells. PthA4 binds to the effector binding elements (EBEs) in the promoter region of canker susceptibility gene LOB1 (EBEPthA4-LOBP) to activate its expression and subsequently cause canker symptoms. Previously, the Cas12a/CBE co-editing method was employed to disrupt EBEPthA4-LOBP of pummelo, which is highly homozygous. However, most commercial citrus cultivars are heterozygous hybrids and more difficult to generate homozygous/biallelic mutants. Here, we employed Cas12a/CBE co-editing method to edit EBEPthA4-LOBP of Hamlin (Citrus sinensis), a commercial heterozygous hybrid citrus cultivar grown worldwide. Binary vector GFP-p1380N-ttLbCas12a:LOBP1-mPBE:ALS2:ALS1 was constructed and shown to be functional via Xcc-facilitated agroinfiltration in Hamlin leaves. This construct allows the selection of transgene-free regenerants via GFP, edits ALS to generate chlorsulfuron-resistant regenerants as a selection marker for genome editing resulting from transient expression of the T-DNA via nCas9-mPBE:ALS2:ALS1, and edits gene(s) of interest (i.e., EBEPthA4-LOBP in this study) through ttLbCas12a, thus creating transgene-free citrus. Totally, 77 plantlets were produced. Among them, 8 plantlets were transgenic plants (#HamGFP1 - #HamGFP8), 4 plantlets were transgene-free (#HamNoGFP1 - #HamNoGFP4), and the rest were wild type. Among 4 transgene-free plantlets, three lines (#HamNoGFP1, #HamNoGFP2 and #HamNoGFP3) contained biallelic mutations in EBEpthA4, and one line (#HamNoGFP4) had homozygous mutations in EBEpthA4. We achieved 5.2% transgene-free homozygous/biallelic mutation efficiency for EBEPthA4–LOBP in C. sinensis cv. Hamlin, compared to 1.9% mutation efficiency for pummelo in a previous study. Importantly, the four transgene-free plantlets and 3 transgenic plantlets that survived were resistant against citrus canker. Taken together, Cas12a/CBE co-editing method has been successfully used to generate transgene-free canker‐resistant C. sinensis cv. Hamlin in the T0 generation via biallelic/homozygous editing of EBEpthA4 of the canker susceptibility gene LOB1.

Abstract Citrus canker caused by Xanthomonas citri subsp. citri (Xcc) is a destructive citrus disease worldwide. Generating disease-resistant cultivars is the most effective, environmentally friendly and economic approach for disease control. However, citrus traditional breeding is lengthy and laborious. Here, we develop transgene-free canker-resistant Citrus sinensis lines in the T0 generation within 10 months through transformation of embryogenic protoplasts with Cas12a/crRNA ribonucleoprotein to edit the canker susceptibility gene CsLOB1. Among the 39 regenerated lines, 38 are biallelic/homozygous mutants, demonstrating a 97.4% biallelic/homozygous mutation rate. No off-target mutations are detected in the edited lines. Canker resistance of the cslob1-edited lines results from both abolishing canker symptoms and inhibiting Xcc growth. The transgene-free canker-resistant C. sinensis lines have received regulatory approval by USDA APHIS and are exempted from EPA regulation. This study provides a sustainable and efficient citrus canker control solution and presents an efficient transgene-free genome-editing strategy for citrus and other crops.

Abstract Background The study aimed to establish a prognostic survival model with 8 pyroptosis-and-cuproptosis-related genes to examine the prognostic effect in patients of hepatocellular carcinoma (HCC). Methods We downloaded gene expression data and clinical information of HCC patients from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO). The clustering analysis and cox regression with LASSO were used for constructing an 8 PCmRNAs survival model. Using TCGA, ICGC and GEO cohort, the overall survival (OS) between high- and low- risk group was determined. We also evaluated independent prognostic indicators using univariate and multivariate analyses. The relatively bioinformatics analysis, including immune cell infiltration, function enrichment and drug sensitivity analyses, was performed as well. The gene expression of 8 PCmRNAs in vitro were validated in several HCC cell lines by qRT-PCR and Western blot. The relationship between GZMA and Fludarabine were further checked by CCK-8 assay. Results The survival prognostic model was constructed with ATP7A, GLS, CDKN2A, BAK1, CHMP4B, NLRP6, NOD1 and GZMA using data from TCGA cohort. The ICGC and GEO cohort were used for model validation. Receiver operating characteristic (ROC) curves showed a good survival prediction by this model. Risk scores had the highest predictable value for survival among Stage, Age, Gender and Grade. Most Immune cells and immune functions were decreased in high-risk group. Besides, function enrichment analyses showed that steroid metabolic process, hormone metabolic process, collagen − containing extracellular matrix, oxidoreductase activity and pyruvate metabolism were enriched. Potential drugs targeted different PCDEGs like Nelarabine, Dexamethasone and Fludarabine were found as well. ATP7A, GLS, CDKN2A, BAK1, CHMP4B, NOD1 were upregulated while NLRP6 and GZMA were downregulated in most HCC cell lines. The potential therapy of Fludarabine was demonstrated when GZMA was low expressed in Huh7 cell line. Conclusion We constructed a novel 8-gene (ATP7A, GLS, CDKN2A, BAK1, CHMP4B, NLRP6, NOD1 and GZMA) prognostic model and explored potential functional information and microenvironment of HCC, which might be worthy of clinical application. In addition, several potential chemotherapy drugs were screened and Fludarabine might be effective for HCC patients whose GZMA was low expressed.

This review explores additive manufacturing (AM) for refractory tungsten (W) and its alloys, highlighting the primary challenges and determining factors in the AM of pure W, W alloys and composites. The challenges mainly arise from W’s high melting point, low laser absorptivity, high thermal conductivity, high melt viscosity, high oxygen affinity, high ductile-to-brittle transition temperature, and inherent embrittlement, which lead to defects and anomalies in AM-produced parts. This review focuses on both processes and alloying strategies to address the issues related to densification, micro-cracking, and the resultant properties in W-based components. Cracking in additively manufactured W remains a persistent issue due to thermal stress, embrittlement, and oxide formation. Powder characteristics, process parameters, and thermal management strategies are crucial for W densification. Throughout the review, existing knowledge and insights are organized into comprehensive tables, serving as valuable resources for researchers delving deeper into this topic. Future research in W-AM should focus on understanding the interaction between AM process parameters and microstructural and material design. Advances in atomic-level understanding, thermodynamic modeling, and data analytics have the potential to significantly enhance the precision, sustainability, and applicability of W-AM.

Wheat scab can reduce wheat yield and quality. Currently, unmanned aerial vehicles (UAVs) are widely used for monitoring field crops. However, UAV is constrained by limited computational resources on-board the platforms. In addition, compared to ground images, UAV images have complex backgrounds and smaller targets. Given the aforementioned challenges, this paper proposes a lightweight wheat scab detection network based on UAV. In addition, overlapping cropping and image contrast enhancement methods are designed to preprocess UAV remote-sensing images. Additionally, this work constructed a lightweight wheat scab detection network called LWSDNet using mixed deep convolution (MixConv) to monitor wheat scab in field environments. MixConv can significantly reduce the parameters of the LWSDNet network through depthwise convolution and pointwise convolution, and different sizes of kernels can extract rich scab features. In order to enable LWSDNet to extract more scab features, a scab feature enhancement module, which utilizes spatial attention and dilated convolution, is designed to improve the ability of the network to extract scab features. The MixConv adaptive feature fusion module is designed to accurately detect lesions of different sizes, fully utilizing the semantic and detailed information in the network to enable more accurate detection by LWSDNet. During the training process, a knowledge distillation strategy that integrates scab features and responses is employed to further improve the average precision of LWSDNet detection. Experimental results demonstrate that the average precision of LWSDNet in detecting wheat scab is 79.8%, which is higher than common object detection models and lightweight object detection models. The parameters of LWSDNet are only 3.2 million (M), generally lower than existing lightweight object detection networks.

Innate immunity, the first line of host defense against viral infections, recognizes viral components through different pattern-recognition receptors. Nucleic acids derived from viruses are mainly recognized by Toll-like receptors, nucleotide-binding domain leucine-rich repeat-containing receptors, absent in melanoma 2-like receptors, and cytosolic DNA sensors (e.g., Z-DNA-binding protein 1 and cyclic GMP-AMP synthase). Different types of nucleic acid sensors can recognize specific viruses due to their unique structures. PANoptosis is a unique form of inflammatory cell death pathway that is triggered by innate immune sensors and driven by caspases and receptor-interacting serine/threonine kinases through PANoptosome complexes. Nucleic acid sensors (e.g., Z-DNA-binding protein 1 and absent in melanoma 2) not only detect viruses, but also mediate PANoptosis through providing scaffold for the assembly of PANoptosomes. This review summarizes the structures of different nucleic acid sensors, discusses their roles in viral infections by driving PANoptosis, and highlights the crosstalk between different nucleic acid sensors. It also underscores the promising prospect of manipulating nucleic acid sensors as a therapeutic approach for viral infections.