Comprehensive genome-wide identification of Snf2 gene family and their expression profile under salt stress in six Brassica species of U's triangle model.

MAIN CONCLUSION: We comprehensively identified and analyzed the Snf2 gene family. Some Snf2 genes were involved in responding to salt stress based on the RNA-seq and qRT-PCR analysis. Sucrose nonfermenting 2 (Snf2) proteins are core components of chromatin remodeling complexes that not only alter DNA accessibility using the energy of ATP hydrolysis, but also play a critical regulatory role in growth, development, and stress response in eukaryotes. However, the comparative study of Snf2 gene family in the six Brassica species in U's triangle model remains unclear. Here, a total of 405 Snf2 genes were identified, comprising 53, 50, and 46 in the diploid progenitors: Brassica rapa (AA, 2n = 20), Brassica nigra (BB, 2n = 16), and Brassica oleracea (CC, 2n = 18), and 93, 91, and 72 in the allotetraploid: Brassica juncea (AABB, 2n = 36), Brassica napus (AACC, 2n = 38), and Brassica carinata (BBCC, 2n = 34), respectively. These genes were classified into six clades and further divided into 18 subfamilies based on their conserved motifs and domains. Intriguingly, these genes showed highly conserved chromosomal distributions and gene structures, indicating that few dynamic changes occurred during the polyploidization. The duplication modes of the six Brassica species were diverse, and the expansion of most Snf2 in Brassica occurred primarily through dispersed duplication (DSD) events. Additionally, the majority of Snf2 genes were under purifying selection during polyploidization, and some Snf2 genes were associated with various abiotic stresses. Both RNA-seq and qRT-PCR analysis showed that the expression of BnaSnf2 genes was significantly induced under salt stress, implying their involvement in salt tolerance response in Brassica species. The results provide a comprehensive understanding of the Snf2 genes in U's triangle model species, which will facilitate further functional analysis of the Snf2 genes in Brassica plants.

Crosstalk between CXCL12/CXCR4/ACKR3 and the STAT3 Pathway.

The reciprocal modulation between the CXCL12/CXCR4/ACKR3 axis and the STAT3 signaling pathway plays a crucial role in the progression of various diseases and neoplasms. Activation of the CXCL12/CXCR4/ACKR3 axis triggers the STAT3 pathway through multiple mechanisms, while the STAT3 pathway also regulates the expression of CXCL12. This review offers a thorough and systematic analysis of the reciprocal regulatory mechanisms between the CXCL12/CXCR4/ACKR3 signaling axis and the STAT3 signaling pathway in the context of diseases, particularly tumors. It explores the potential clinical applications in tumor treatment, highlighting possible therapeutic targets and novel strategies for targeted tumor therapy.

Revealing Brownish Mycena Diversity in China: New Discoveries and Taxonomic Insights.

Within the genus Mycena, species exhibiting brownish basidiomata present considerable challenges in identification due to similar coloration. This study underscores the significance of pileipellis types and cheilocystidia characteristics as critical in delimiting brownish Mycena species. To clarify the principal taxonomic characters and their utility in distinguishing between brownish Mycena species, a morphological taxonomy and phylogenetic analysis were performed. Five new species from China were introduced and characterized through a comprehensive morphological anatomy and phylogenetic substantiation: M. campanulatihemisphaerica sp. nov., M. digitifurcata sp. nov., M. kunyuensis sp. nov., M. limitis sp. nov., and M. oryzifluens sp. nov. Discussions of these taxa are supplemented with morphological illustrations. The phylogenetic relationships were inferred using Bayesian Inference and Maximum Likelihood methods based on sequences from the internal transcribed spacer and the large subunit regions of nuclear ribosomal RNA. With the addition of these five new species, the worldwide count of brownish Mycena increases to 94, and a key to the 29 known species of brownish Mycena from China is presented.

Shear wave trajectory detection in ultra-fast M-mode images for liver fibrosis assessment: A deep learning-based line detection approach.

Stiffness measurement using shear wave propagation velocity has been the most common non-invasive method for liver fibrosis assessment. The velocity is captured through a trace recorded by transient ultrasonographic elastography, with the slope indicating the velocity of the wave. However, due to various factors such as noise and shear wave attenuation, detecting shear wave trajectory on wave propagation maps is a challenging task. In this work, we made the first attempt to use deep learning methods for shear wave trajectory detection on wave propagation maps. Specifically, we adopted five deep learning models in this task and evaluated them by using a well-acknowledged metric based on EA-Angular-Score (EAA) and task-specific metric based on Young s-Score (Ys) in the line-detection field. Furthermore, we proposed an end-to-end framework based on a Transformer and Hough transform, named Transformer-enhanced Hough Transform (TEHT). It took a wave propagation map as input image and directly output the slope of the shear wave trajectory. The framework extracts multi-scale local features from wave propagation maps, employs a deformable attention mechanism for feature fusion, identifies the target line using the Hough transform's voting mechanism, and calculates the contribution of each scale through channel attention. Wave propagation maps from 68 patients were utilized in this study, with manual annotation performed by a rater who was trained as a radiologist, serving as the reference value. The evaluation revealed that the SLNet model exhibited F-measure of EA and Ys values as 40.33 % and 40.72 %, respectively, while the TEHT model showed F-measure of EA and Ys values as 80.96 % and 98.00 %, respectively. TEHT yielded significantly better performance than other deep learning models. Moreover, TEHT demonstrated strong concordance with the gold standard, yielding R2 values of 0.967 and 0.968 for velocity and liver stiffness, respectively. The present study therefore suggests the application of the TEHT model for assessing liver fibrosis owing to its superiority among the five deep learning models.

A dual-site fluorescent probe for the detection of γ-glutamyl transpeptidase activity and its application in garlic.

Developing convenient γ-glutamyl transpeptidase (GGT) activity detection methods is of great significance for soaking Laba garlic and human diseases detection. A dual-site fluorescent probe (probe 1) was developed for detection the activity of GGT. Probe 1 could recognize GGT by the enzymatic hydrolysis of peptide bond by GGT. There has a linear relationship between the fluorescence intensity of probe 1 at 416 nm and the activity of GGT. And the color of the probe solution gradually changed from colorless to blue with the increase of GGT activity under 365 nm ultraviolet light. Importantly, it has a linear relationship between the activity of GGT and the blue (B) value of probe solution photo. Therefore, probes can serve as a convenient tool for detecting GGT activity. More importantly, the probe has been successfully applied to detect of GGT activity in garlic.

Protecting primary teeth from dental erosion through bioactive glass.

OBJECTIVES: The present study aimed to evaluate the effectiveness of bioactive glass (BAG) in preventing dental erosion in primary teeth. METHODS: Enamel and dentin specimens (2 × 2 × 2 mm) were obtained from extracted primary teeth, which were randomly divided into the following groups based on the pretreatments (n = 12): DW (deionized water), NaF (2 % sodium fluoride), 2BAG (2 % BAG), 4BAG (4 % BAG), 6BAG (6 % BAG), and 8BAG (8 % BAG). The specimens were immersed in the respective solutions for 2 min and subjected to in vitro erosive challenges (4 × 5 min/d) for 5 d. The erosive enamel loss (EEL), erosive dentin loss (EDL), and the thickness of the demineralized organic matrix (DOM) were measured using a contact profilometer. The surface microhardness (SMH) was measured, and the percentage of SMH loss (%SMHL) was calculated. The surface morphology and mineral composition were evaluated by scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS), respectively. RESULTS: After the erosive challenges, the EEL, EDL, and%SMHL of the 2BAG, 4BAG, 6BAG, and 8BAG groups significantly reduced, with the greatest reduction was observed in the 6BAG (EEL: 6.5 ± 0.2 µm;%SMHL in enamel: 12.8 ± 2.6; EDL: 7.9 ± 0.3 µm; %SMHL in dentin: 22.1 ± 2.7) and 8BAG groups (EEL: 6.4 ± 0.4 µm;%SMHL in enamel: 11.0 ± 1.9; EDL: 7.8 ± 0.5 µm; %SMHL in dentin: 22.0 ± 2.5) (P < 0.05). With increasing BAG concentrations, the number of surface deposits containing Ca, P, and Si increased. CONCLUSIONS: 6BAG was the most effective for preventing dental erosion in primary teeth and showed a particularly strong potential for dentin erosion prevention. CLINICAL SIGNIFICANCE: Bioactive glass, especially at a 6 % concentration, has proven effective in reducing erosive tooth wear and surface microhardness loss while also protecting demineralized organic matrix in primary dentin.

LoRA-TV: read depth profile-based clustering of tumor cells in single-cell sequencing.

Single-cell sequencing has revolutionized our ability to dissect the heterogeneity within tumor populations. In this study, we present LoRA-TV (Low Rank Approximation with Total Variation), a novel method for clustering tumor cells based on the read depth profiles derived from single-cell sequencing data. Traditional analysis pipelines process read depth profiles of each cell individually. By aggregating shared genomic signatures distributed among individual cells using low-rank optimization and robust smoothing, the proposed method enhances clustering performance. Results from analyses of both simulated and real data demonstrate its effectiveness compared with state-of-the-art alternatives, as supported by improvements in the adjusted Rand index and computational efficiency.

Genome-wide identification of the ICS family genes and its role in resistance to Plasmodiophora brassicae in Brassica napus L.

The isochorismate synthase (ICS) proteins are essential regulators of salicylic acid (SA) synthesis, which has been reported to regulate resistance to biotic and abiotic stresses in plants. Clubroot caused by Plasmodiophora brassicae is a common disease that threatens the yield and quality of Oilseed rape (Brassica napus L.). Exogenous application of salicylic acid reduced the incidence of clubroot in oilseed rape. However, the potential importance of the ICS genes family in B. napus and its diploid progenitors has been unclear. Here, we identified 16, 9, and 10 ICS genes in the allotetraploid B. napus, diploid ancestor Brassica rapa and Brassica oleracea, respectively. These ICS genes were classified into three subfamilies (I-III), and member of the same subfamilies showed relatively conserved gene structures, motifs, and protein domains. Furthermore, many hormone-response and stress-related promoter cis-acting elements were observed in the BnaICS genes. Exogenous application of SA delayed the growth of clubroot galls, and the expression of BnaICS genes was significantly different compared to the control groups. Protein-protein interaction analysis identified 58 proteins involved in the regulation of ICS in response to P. brassicae in B. napus. These results provide new clues for understanding the resistance mechanism to P. brassicae.

Capsaicin reduces blood glucose and prevents prostate growth by regulating androgen, RAGE/IGF-1/Akt, TGF-ß/Smad signalling pathway and reversing epithelial-mesenchymal transition in streptozotocin-induced diabetic mice.

Type 2 diabetes mellitus (T2DM) is a metabolic disease. Diabetes increases the risk of benign prostatic hyperplasia (BPH). Capsaicin is extracted from chili peppers and possesses many pharmacological properties, including anti-diabetic, pain-relieving, and anti-cancer properties. This study aimed to investigate the effects of capsaicin on glucose metabolism and prostate growth in T2DM mice and uncover the related mechanisms. Mice model of diabetes was established by administering a high-fat diet and streptozotocin. Oral administration of capsaicin for 2 weeks inhibited prostate growth in testosterone propionate (TP)-treated mice. Furthermore, oral administration of capsaicin (5 mg/kg) for 2 weeks decreased fasting blood glucose, prostate weight, and prostate index in diabetic and TP-DM mice. Histopathological alterations were measured using hematoxylin & eosin (H&E) staining. The protein expression of 5α-reductase type II, androgen receptor (AR), and prostate-specific antigen (PSA) were upregulated in diabetic and TP-DM mice, but capsaicin reversed these effects. Capsaicin decreased the protein expression of p-AKT, insulin-like growth factor-1 (IGF-1), IGF-1R, and the receptor for advanced glycation end products (RAGE) in diabetic and TP-DM mice. Capsaicin also regulated epithelial-mesenchymal transition (EMT) and modulated the expression of fibrosis-related proteins, including E-cadherin, N-cadherin, vimentin, fibronectin, α-SMA, TGFBR2, TGF-ß1, and p-Smad in TP-DM mice. In this study, capsaicin alleviated diabetic prostate growth by attenuating EMT. Mechanistically, capsaicin affected EMT by regulating RAGE/IGF-1/AKT, AR, and TGF-ß/Smad signalling pathways. These results provide with new therapeutic approach for treating T2DM or T2DM-induced prostate growth.

A wireless controlled robotic insect with ultrafast untethered running speeds.

Running speed degradation of insect-scale (less than 5 cm) legged microrobots after carrying payloads has become a bottleneck for microrobots to achieve high untethered locomotion performance. In this work, we present a 2-cm legged microrobot (BHMbot, BeiHang Microrobot) with ultrafast untethered running speeds, which is facilitated by the complementary combination of bouncing length and bouncing frequency in the microrobot's running gait. The untethered BHMbot (2-cm-long, 1760 mg) can achieve a running speed of 17.5 BL s-1 and a turning centripetal acceleration of 65.4 BL s-2 at a Cost of Transport of 303.7 and a power consumption of 1.77 W. By controlling its two front legs independently, the BHMbot demonstrates various locomotion trajectories including circles, rectangles, letters and irregular paths across obstacles through a wireless control module. Such advancements enable the BHMbot to carry out application attempts including sound signal detection, locomotion inside a turbofan engine and transportation via a quadrotor.

Research Progress on the Application of Multifunctional Amino Derivative Fluorescent Probes in Food, the Environment, and the Microenvironment.

The amino group is regarded as a multifunctional recognition group in fluorescent probes. It is nucleophilic, a strong electron-donating group and is a polar group with active hydrogen. Based on these characteristics, amino-based fluorescent probes combined with various fluorescent precursors have been constructed, with excellent sensing performance and low cytotoxicity. These probes have significant application value in the detection of food, living cells and organisms. Here, the relevant studies on amino fluorescent probes from 2016 to 2024 are systematically reviewed and their molecular design principles, recognition mechanisms and applications are described. These studies included 14 on exogenous and endogenous formaldehyde detection, five that detected polarity changes in the external environment and organelles in vivo, four intracellular mitochondrial and lysosomal viscosity detections, seven physiological environment and intracellular pH detections, seven metal ion detections in biological and environmental systems and four rapid detections of the hypochlorite anion (ClO-) in a variety of physiological processes and cells. The application scope of amino fluorescent probes is constantly expanding at present but, research progress in multiple application fields has not been summarized. This article mainly reviews the latest progress in amino fluorescent probes in the fields of food, the environment and the microenvironment, as well as looking forward to the development prospects of these fluorescent probes. Improving the reactivity of amino recognition groups and visual detection may become hot issues in future research.

Clustering algorithm based on DINNSM and its application in gene expression data analysis.

BACKGROUND: Selecting an appropriate similarity measurement method is crucial for obtaining biologically meaningful clustering modules. Commonly used measurement methods are insufficient in capturing the complexity of biological systems and fail to accurately represent their intricate interactions. OBJECTIVE: This study aimed to obtain biologically meaningful gene modules by using the clustering algorithm based on a similarity measurement method. METHODS: A new algorithm called the Dual-Index Nearest Neighbor Similarity Measure (DINNSM) was proposed. This algorithm calculated the similarity matrix between genes using Pearson's or Spearman's correlation. It was then used to construct a nearest-neighbor table based on the similarity matrix. The final similarity matrix was reconstructed using the positions of shared genes in the nearest neighbor table and the number of shared genes. RESULTS: Experiments were conducted on five different gene expression datasets and compared with five widely used similarity measurement techniques for gene expression data. The findings demonstrate that when utilizing DINNSM as the similarity measure, the clustering results performed better than using alternative measurement techniques. CONCLUSIONS: DINNSM provided more accurate insights into the intricate biological connections among genes, facilitating the identification of more accurate and biological gene co-expression modules.

Alternative polyadenylation quantitative trait loci contribute to acute myeloid leukemia risk genes regulation.

Acute myeloid leukemia (AML) is a hematopoietic malignancy with a high relapse rate and progressive drug resistance. Alternative polyadenylation (APA) contributes to post-transcriptional dysregulation, but little is known about the association between APA and AML. The APA quantitative trait locus (apaQTL) is a powerful method to investigate the relationship between APA and single nucleotide polymorphisms (SNPs). We quantified APA usage in 195 Chinese AML patients and identified 4922 cis-apaQTLs related to 1875 genes, most of which were newly reported. Cis-apaQTLs may modulate the APA selection of 115 genes through poly(A) signals. Colocalization analysis revealed that cis-apaQTLs colocalized with cis-eQTLs may regulate gene expression by affecting miRNA binding sites or RNA secondary structures. We discovered 207 cis-apaQTLs related to AML risk by comparing genotype frequency with the East Asian healthy controls from the 1000 Genomes Project. Genes with cis-apaQTLs were associated with hematological phenotypes and tumor incidence according to the PHARMGKB and MGI databases. Collectively, we profiled an atlas of cis-apaQTLs in Asian AML patients and found their association with APA selection, gene expression, AML risk, and complex traits. Cis-apaQTLs may provide insights into the regulatory mechanisms related to APA in AML occurrence, progression, and prognosis.

Analysis of m6A-related lncRNAs for prognostic and immunotherapeutic response in hepatocellular carcinoma.

Background: RNA methylation modifications are important post-translational modifications that are regulated in an epigenetic manner. Recently, N6-methyladenosine (m6A) RNA modifications have emerged as potential epigenetic markers in tumor biology. Methods: Gene expression and clinicopathological data of LIHC were obtained from the cancer genome atlas (TCGA) database. The relationship between long non-coding RNAs (lncRNAs) and m6A-related genes was determined by gene expression analysis using Perl and R software. Co-expression network of m6A-lncRNA was constructed, and the relevant lncRNAs associated with prognosis were identified using univariate Cox regression analysis. These lncRNAs were then divided into two clusters (cluster 1 and cluster 2) to determine the differences in survival, pathoclinical parameters, and immune cell infiltration between the different lncRNA subtypes. The least absolute shrinkage and selection operator (LASSO) was carried out for regression analysis and prognostic model. The HCC patients were randomly divided into a train group and a test group. According to the median risk score of the model, HCC patients were divided into high-risk and low-risk groups. We built models using the train group and confirmed them through the test group. The m6A-lncRNAs derived from the models were analyzed for the tumor mutational burden (TMB), immune evasion and immune function using R software. AL355574.1 was identified as an important m6A-associated lncRNA and selected for further investigation. Finally, in vitro experiments were conducted to confirm the effect of AL355574.1 on the biological function of HCC and the possible biological mechanisms. Huh7 and HepG2 cells were transfected with AL355574.1 siRNA and cell proliferation ability was measured by CCK-8, EdU and colony formation assays. Wound healing and transwell assays were used to determine the cell migration capacity. The expression levels of MMP-2, MMP-9, E-cadherin, N-cadherin and Akt/mTOR phosphorylation were all determined by Western blotting. Results: The lncRNAs with significant prognostic value were classified into two subtypes by a consistent clustering analysis. We found that the clinical features, immune cell infiltration and tumor microenvironment (TME) were significantly different between the lncRNA subtypes. Our analysis revealed significant correlations between these different lncRNA subtypes and immune infiltrating and stromal cells. We created the final risk profile using LASSO regression, which notably included three lncRNAs (AL355574.1, AL158166.1, TMCC1-AS1). A prognostic signature consisting of the three lncRNAs was constructed, and the model showed excellent prognostic predictive ability. The overall survival (OS) of the low-risk cohort was significantly higher than that of the high-risk cohort in both the train and test group. Both risk score [hazard ratio (HR)=1.062; P<0.001] and stage (HR=1.647; P< 0.001) were considered independent indicators of HCC prognosis by univariate and multivariate Cox regression analysis. In Huh7 and HepG2 cells, AL355574.1 knockdown inhibited cell proliferation and migration, suppressed the protein expression levels of MMP-2, MMP-9, N-cadherin and Akt/mTOR phosphorylation, but promoted the protein expression levels of E-cadherin. Conclusions: This study established a predictive model for the OS of HCC patients, and these OS-related m6A-lncRNAs, especially AL355574.1 may play a potential role in the progression of HCC. In vitro experiments also showed that AL355574.1 could enhance the expression of MMPs and EMT through the Akt/mTOR signaling pathway, thereby affected the proliferation and migration of HCC. This provides a new perspective on the anticancer molecular mechanism of AL355574.1 in HCC.

Root system architecture change in response to waterlogging stress in a 448 global collection of rapeseeds (Brassica napus L.).

MAIN CONCLUSIONS: A novel image-based screening method for precisely identifying genotypic variations in rapeseed RSA under waterlogging stress was developed. Five key root traits were confirmed as good indicators of waterlogging and might be employed in breeding, particularly when using the MFVW approach. Waterlogging is a vital environmental factor that has detrimental effects on the growth and development of rapeseed (Brassica napus L.). Plant roots suffer from hypoxia under waterlogging, which ultimately confers yield penalty. Therefore, it is crucially important to understand the genetic variation of root system architecture (RSA) in response to waterlogging stress to guide the selection of new tolerant cultivars with favorable roots. This research was conducted to investigate RSA traits using image-based screening techniques to better understand how RSA changes over time during waterlogging at the seedling stage. First, we performed a t-test by comparing the relative root trait value between four tolerant and four sensitive accessions. The most important root characteristics associated with waterlogging tolerance at 12 h are total root length (TRL), total root surface area (TRSA), total root volume (TRV), total number of tips (TNT), and total number of forks (TNF). The root structures of 448 rapeseed accessions with or without waterlogging showed notable genetic diversity, and all traits were generally restrained under waterlogging conditions, except for the total root average diameter. Additionally, according to the evaluation and integration analysis of 448 accessions, we identified that five traits, TRL, TRSA, TRV, TNT, and TNF, were the most reliable traits for screening waterlogging-tolerant accessions. Using analysis of the membership function value (MFVW) and D-value of the five selected traits, 25 extremely waterlogging-tolerant materials were screened out. Waterlogging significantly reduced RSA, inhibiting root growth compared to the control. Additionally, waterlogging increased lipid peroxidation, accompanied by a decrease in the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). This study effectively improves our understanding of the response of RSA to waterlogging. The image-based screening method developed in this study provides a new scientific guidance for quickly examining the basic RSA changes and precisely predicting waterlogging-tolerant rapeseed germplasms, thus expanding the genetic diversity of waterlogging-tolerant rapeseed germplasm available for breeding.

Arylacryl amides: Design, synthesis and the protection against cisplatin-induced acute kidney injury via TLR4/STING/NF-κB pathway.

Arylpropionic ester scaffold was found as anti-inflammatory agents for the treatment and prevention of acute kidney injury (AKI). To further study the structure-activity relationship (SAR) of this scaffold, a series of acryl amides were designed, synthesized, and evaluated their anti-inflammation. Of these, compound 9d displayed the protective effect on renal tubular epithelial cells to significantly enhance the survival rate through inhibiting NF-κB phosphorylation and promoting cell proliferation in cisplatin-induced HK2 cells. Furthermore, 9d can interact with TLR4 to inhibit TLR4/STING/NF-κB pathway in the RAW264.7 cell. In vivo AKI mice model, 9d significantly downregulated the level of serum creatinine (Scr), blood urea nitrogen (BUN) and the inflammatory factors (IL-1ß, IL-6, TNF-α) to improve kidney function. Morphological and KIM-1 analyses showed that 9d alleviated cisplatin-induced tubular damage. In a word, 9d was a promising lead compound for preventive and therapeutic of AKI.

Connective tissue disorders in COVID-19: Reply to "People with a connective tissue disorder may be especially vulnerable to the endothelial damage that characterizes long COVID due to the fragility of their vasculature and slow wound healing".

Connective tissue serves as a framework for other tissues and organs, supporting their functions, shielding them from harmful factors, and aiding repair. In COVID-19, damaged endothelial cells (ECs), increased endothelial permeability, and thrombi contribute to the connective tissue disorders. Even post-recovery, the damage to ECs and connective tissues persists, resulting in long COVID. Individuals with connective tissue disorders are prone to developing severe COVID-19 and experiencing long COVID symptoms. It is advised that these patients receive at least three vaccine doses, undergo early prophylactic antithrombotic therapy during acute COVID-19, and maintain prophylactic anticoagulant treatment in cases of long COVID.

A new chromosome-scale genome of wild Brassica oleracea provides insights into the domestication of Brassica crops.

The cultivated diploid Brassica oleracea is an important vegetable crop, but the genetic basis of its domestication remains largely unclear in the absence of high-quality reference genomes of wild B. oleracea. Here, we report the first chromosome-level assembly of the wild Brassica oleracea L. W03 genome (total genome size, 630.7 Mb; scaffold N50, 64.6 Mb). Using the newly assembled W03 genome, we constructed a gene-based B. oleracea pangenome and identified 29 744 core genes, 23 306 dispensable genes, and 1896 private genes. We re-sequenced 53 accessions, representing six potential wild B. oleracea progenitor species. The results of the population genomic analysis showed that the wild B. oleracea populations had the highest level of diversity and represents the most closely related population to modern-day horticultural B. oleracea. In addition, the WUSCHEL gene was found to play a decisive role in domestication and to be involved in cauliflower and broccoli curd formation. We also illustrate the loss of disease-resistance genes during selection for domestication. Our results provide new insights into the domestication of B. oleracea and will facilitate the future genetic improvement of Brassica crops.

A comparison of [18F]AlF- and 68Ga-labeled dual targeting heterodimer FAPI-RGD in malignant tumor: preclinical evaluation and pilot clinical PET/CT imaging.

Due to the heterogeneity of tumors, strategies to improve the effectiveness of dual-targeting tracers in tumor diagnostics have been intensively practiced. In this study, the radiolabeled [18F]AlF-NOTA-FAPI-RGD (denoted as [18F]AlF-LNC1007), a dual-targeting heterodimer tracer targeting both fibroblast activation protein (FAP) and integrin αvß3 to enhance specific tumor uptake and retention, was synthesized and evaluated. The tracer was compared with [68Ga]Ga-LNC1007 in preclinical and clinical settings. METHODS: The preparation of [18F]AlF- and 68Ga-labeled FAPI-RGD was carried out with an optimized protocol. The stability was tested in PBS and fetal bovine serum (FBS). Cellular uptake and in vivo distribution of the two products were compared and carried out on the U87MG cell line and its xenograft model. The safety and dosimetry of [18F]AlF-LNC1007 PET/CT scan were evaluated in six patients with malignant tumors. RESULTS: Two radiolabeling protocols of [18F]AlF-/[68Ga]Ga-LNC1007 were developed and optimized to give a high yield of tracers with good stability. In vivo microPET images showed that the two tracers exhibited comparable pharmacokinetic characteristics, with high tumor uptake and prolonged tumor retention. In vivo distribution data showed that the target-to-non-target ratios of [18F]AlF-LNC1007 were similar to[68Ga]Ga-LNC1007. A total of six patients underwent [18F]AlF-LNC1007 PET/CT evaluation while two had head-to-head [18F]FDG PET/CT scans. The total body effective dose was 9.94E-03 mSv/MBq. The biodistribution curve showed optimal normal organ uptake with high tumor uptake and long retention of up to 3h p.i., and notably, the tumor-to-background ratio increased over time. CONCLUSION: We successfully prepared an [18F]AlF-LNC1007 dual-targeting PET probe with comparable performances as [68Ga]Ga-LNC1007. With prolonged tumor retention and tumor specificity, it produced good imaging quality in preclinical and clinical translational studies, indicating that [18F]AlF-LNC1007 is a promising non-invasive tracer for detecting tumors expressing FAP and/or integrin avß3, with the prospect of clinical implementation.

Systematic analysis of the role of LDHs subtype in pan-cancer demonstrates the importance of LDHD in the prognosis of hepatocellular carcinoma patients.

BACKGROUND: Lactate dehydrogenase (LDHs) is an enzyme involved in anaerobic glycolysis, including LDHA, LDHB, LDHC and LDHD. Given the regulatory role in the biological progression of certain tumors, we analyzed the role of LDHs in pan-cancers. METHODS: Cox regression, Kaplan-Meier curves, Receiver Operating Characteristic (ROC) curves, and correlation of clinical indicators in tumor patients were used to assess the prognostic significance of LDHs in pan-cancer. The TCGA, HPA, TIMER, UALCAN, TISIDB, and Cellminer databases were used to investigate the correlation between the expression of LDHs and immune subtypes, immune checkpoint genes, methylation levels, tumor mutational load, microsatellite instability, tumor-infiltrating immune cells and drug sensitivity. The cBioPortal database was also used to identify genomic abnormalities of LDHs in pan-cancer. A comprehensive assessment of the biological functions of LDHs was performed using GSEA. In vitro, HepG2 and Huh7 cells were transfected with LDHD siRNA and GFP-LDHD, the proliferation capacity of cells was examined using CCK-8, EdU, and colony formation assays; the migration and invasion of cells was detected by wound healing and transwell assays; western blotting was used to detect the levels of MMP-2, MMP-9, E-cadherin, N-cadherin and Akt phosphorylation. RESULTS: LDHs were differentially expressed in a variety of human tumor tissues. LDHs subtypes can act as pro-oncogenes or anti-oncogenes in different types of cancer and have an impact on the prognosis of patients with tumors by influencing their clinicopathological characteristics. LDHs were differentially expressed in tumor immune subtypes and molecular subtypes. In addition, LDHs expression correlated with immune checkpoint genes, tumor mutational load, and microsatellite instability. LDHD was identified to play an important role in the prognosis of HCC patients, according to a comprehensive analysis of LDHs in pan-cancer. In HepG2 and Huh7 cells, knockdown of LDHD promoted cell proliferation, migration, and invasion, promoted the protein expression levels of MMP-2, MMP-9, N-cadherin, and Akt phosphorylation, but inhibited the protein expression level of E-cadherin. In addition, LDHD overexpression showed the opposite changes. CONCLUSION: LDHs subtypes can be used as potential prognostic markers for certain cancers. Prognostic and immunotherapeutic analysis indicated that LDHD plays an important role in the prognosis of HCC patients. In vitro experiments revealed that LDHD can affect HCC proliferation, migration, and invasion by regulating MMPs expression and EMT via Akt signaling pathway, which provides a new perspective on the anti-cancer molecular mechanism of LDHD in HCC.