Graph-Based Bidirectional Transformer Decision Threshold Adjustment Algorithm for Class-Imbalanced Molecular Data.

Data sets with imbalanced class sizes, often where one class size is much smaller than that of others, occur extremely often in various applications, including those with biological foundations, such as drug discovery and disease diagnosis. Thus, it is extremely important to be able to identify data elements of classes of various sizes, as a failure to detect can result in heavy costs. However, many data classification algorithms do not perform well on imbalanced data sets as they often fail to detect elements belonging to underrepresented classes. In this paper, we propose the BTDT-MBO algorithm, incorporating Merriman-Bence-Osher (MBO) techniques and a bidirectional transformer, as well as distance correlation and decision threshold adjustments, for data classification problems on highly imbalanced molecular data sets, where the sizes of the classes vary greatly. The proposed method not only integrates adjustments in the classification threshold for the MBO algorithm in order to help deal with the class imbalance, but also uses a bidirectional transformer model based on an attention mechanism for self-supervised learning. Additionally, the method implements distance correlation as a weight function for the similarity graph-based framework on which the adjusted MBO algorithm operates. The proposed model is validated using six molecular data sets, and we also provide a thorough comparison to other competing algorithms. The computational experiments show that the proposed method performs better than competing techniques even when the class imbalance ratio is very high.

YZL-51N functions as a selective inhibitor of SIRT7 by NAD+ competition to impede DNA damage repair.

The NAD+-dependent deacetylase SIRT7 is a pivotal regulator of DNA damage response (DDR) and a promising drug target for developing cancer therapeutics. However, limited progress has been made in SIRT7 modulator discovery. Here, we applied peptide-based deacetylase platforms for SIRT7 enzymatic evaluation and successfully identified a potent SIRT7 inhibitor YZL-51N. We initially isolated bioactive YZL-51N from cockroach (Periplaneta americana) extracts and then developed the de novo synthesis of this compound. Further investigation revealed that YZL-51N impaired SIRT7 enzymatic activities through occupation of the NAD+ binding pocket. YZL-51N attenuated DNA damage repair induced by ionizing radiation (IR) in colorectal cancer cells and exhibited a synergistic anticancer effect when used in combination with etoposide. Overall, our study not only identified YZL-51N as a selective SIRT7 inhibitor from insect resources, but also confirmed its potential use in combined chemo-radiotherapy by interfering in the DNA damage repair process.

Kinetic nitrogen isotope effects of 18 amino acids degradation during burning processes.

Understanding the nitrogen isotopic variations of individual amino acids (AAs) is essential for utilizing the nitrogen isotope values of individual amino acids (δ15N-AA) as source indicators to identify proteinaceous matter originating from biomass combustion processes. However, the nitrogen isotope effects (ε) associated with the degradation of individual amino acids during combustion processes have not been previously explored. In this study, we measured the nitrogen isotope values of residual free amino acids -following a series of controlled combustion experiments at temperatures of 160-240 °C and durations of 2 min to 8 h, as described in Part 1. δ15N values of proline, aspartate, alanine, valine, glycine, leucine, and isoleucine are more positive than their initial δ15N values after prolonged combustion. Variations in δ15N values of the most AAs conform to the Rayleigh fractionation during combustion and their nitrogen isotope effects (ε) are greatly impacted by their respective combustion degradation pathways. This is the first time the ε values associated with the degradation pathways of AAs during combustion have been characterized. Only the ε values associated with Pathway 1 (dehydration to form dipeptide) and 2 (simultaneous deamination and decarboxylation) are found to be significant and temperature-dependent, ranging from + 2.9 to 6.4‰ and + 0.9‰ to + 3.8‰, respectively. Conversely, ε values associated with other pathways are minor. This improves the current understanding on the degradation mechanisms of protein nitrogen during biomass burning.

Chromosome-level genome assembly of a cliff plant Taihangia rupestris var. ciliata provides insights into its adaptation and demographic history.

BACKGROUND: Cliffs are recognized as one of the most challenging environments for plants, characterized by harsh conditions such as drought, infertile soil, and steep terrain. However, they surprisingly host ancient and diverse plant communities and play a crucial role in protecting biodiversity. The Taihang Mountains, which act as a natural boundary in eastern China, support a rich variety of plant species, including many unique to cliff habitats. However, it is little known how cliff plants adapt to harsh habitats and the demographic history in this region. RESULTS: To better understand the demographic history and adaptation of cliff plants in this area, we analyzed the chromosome-level genome of a representative cliff plant, T. rupestris var. ciliata, which has a genome size of 769.5 Mb, with a scaffold N50 of 104.92 Mb. The rapid expansion of transposable elements may have contributed to the increasing genome and its ability to adapt to unique and challenging cliff habitats. Comparative analysis of the genome evolution between Taihangia and non-cliff plants in Rosaceae revealed a significant expansion of gene families associated with oxidative phosphorylation, which is likely a response to the abiotic stresses faced by cliff plants. This expansion may explain the long-term adaptation of Taihangia to harsh cliff environments. The effective population size of the two varieties has continuously decreased due to climatic fluctuations during the Quaternary period. Furthermore, significant differences in gene expression between the two varieties may explain the varied leaf phenotypes and adaptations to harsh conditions in different natural distributions. CONCLUSION: Our study highlights the extraordinary adaptation of T. rupestris var. ciliata, shedding light on the evolution of cliff plants worldwide.

Essentials of CAR-T Therapy and Associated Microbial Challenges in Long Run Immunotherapy.

Chimeric antigen receptor (CAR)-T cell therapy has shown potential in improving outcomes for individuals with hematological malignancies. However, achieving long-term full remission for blood cancer remains challenging due to severe life-threatening toxicities such as limited anti-tumor efficacy, antigen escape, trafficking restrictions, and limited tumor invasion. Furthermore, the interactions between CAR-T cells and their host tumor microenvironments have a significant impact on CAR-T function. To overcome these considerable hurdles, fresh methodologies and approaches are needed to produce more powerful CAR-T cells with greater anti-tumor activity and less toxicity. Despite advances in CAR-T research, microbial resistance remains a significant obstacle. In this review, we discuss and describe the basics of CAR-T structures, generations, challenges, and potential risks of infections in CAR-T cell therapy.

Impacts of LNAPL types on mechanisms and rate of natural source zone depletion.

Understanding the mechanisms of natural source zone depletion (NSZD) will support an improved understanding of the long-term sustainability of NSZD as a site remedy and how NSZD rates may change over time. This is the first study that has quantified and compared the rate of three NSZD mechanisms (methanogenesis, vaporization, and aqueous biodegradation) between two chemically distinct light non-aqueous phase liquid (LNAPL) source zones (aliphatic-rich naphtha for Zone #1 vs aromatic-rich pyrolysis gasoline for Zone #2) within the same geologic and climate conditions. The rates of NSZD attributable to vaporization (400 mg C/m2/d vs. 300 mg C/m2/d) and aqueous biodegradation (92 mg C/m2/d vs. 67 mg C/m2/d) were similar for Zone #1 and #2; however, the rate of methanogenesis NSZD was 6x higher in Zone #1 (1000 mg C/m2/d vs. 170 mg C/m2/d). These results suggest that the aliphatic hydrocarbons content in an LNAPL source may be a factor in the rate of methanogenesis NSZD. For both Zone #1 and #2, total NSZD rate determined using this "three mechanism" measurement method was in reasonable agreement with two other methods used to measure total NSZD rates (CO2 Gradient Method and Dynamic Closed Chamber Method), validating the "three mechanism" method as a tool to measure the total NSZD rate at a site and to provide an improved understanding of the predominant NSZD mechanism. Overall, this study highlights the importance of LNAPL type and chemical characteristics in determining source zone natural attenuation mechanism and its total rates.

Research on spatial carving method of glutenite reservoir based on opacity voxel imaging.

The glutenite reservoir in an exploration area in eastern China is well-developed and holds significant exploration potential as an important oil and gas alternative layer. However, due to the influence of sedimentary characteristics, the glutenite reservoir exhibits strong lateral heterogeneity, significant vertical thickness variations, and low accuracy in reservoir space characterization, which affects the reasonable and effective deployment of development wells. Seismic data contains the three-dimensional spatial characteristics of geological bodies, but how to design a suitable transfer function to extract the nonlinear relationship between seismic data and reservoirs is crucial. At present, the transfer functions are concentrated in low-dimensional or high-dimensional fixed mathematical models, which cannot accurately describe the nonlinear relationship between seismic data and complex reservoirs, resulting in low spatial description accuracy of complex reservoirs. In this regard, this paper first utilizes a fusion method based on probability kernel to fuse seismic attributes such as wave impedance, effective bandwidth, and composite envelope difference. This provide a more intuitive reflection of the distribution characteristics of glutenite reservoirs. Moreover, a hybrid nonlinear transfer function is established to transform the fused attribute cube into an opaque attribute cube. Finally, the illumination model and ray casting method are used to perform voxel imaging of the glutenite reservoirs, brighten the detailed characteristics of reservoir space, and then form a set of methods for ' brightening reservoirs and darkening non-reservoirs ', which improves the spatial engraving accuracy of glutenite reservoirs.

Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation.

AlphaFold 3 (AF3), the latest version of protein structure prediction software, goes beyond its predecessors by predicting protein-protein complexes. It could revolutionize drug discovery and protein engineering, marking a major step towards comprehensive, automated protein structure prediction. However, independent validation of AF3's predictions is necessary. Evaluated using the SKEMPI 2.0 database which involves 317 protein-protein complexes and 8338 mutations, AF3 complex structures give rise to a very good Pearson correlation coefficient of 0.86 for predicting protein-protein binding free energy changes upon mutation, slightly less than the 0.88 achieved earlier with the Protein Data Bank (PDB) structures. Nonetheless, AF3 complex structures led to a 8.6% increase in the prediction RMSE compared to original PDB complex structures. Additionally, some of AF3's complex structures have large errors, which were not captured in its ipTM performance metric. Finally, it is found that AF3's complex structures are not reliable for intrinsically flexible regions or domains.

DRPSO:A multi-strategy fusion particle swarm optimization algorithm with a replacement mechanisms for colon cancer pathology image segmentation.

Colon adenocarcinoma (COAD) is a type of colon cancers with a high mortality rate. Its early symptoms are not obvious, and its late stage is accompanied by various complications that seriously endanger patients' lives. To assist in the early diagnosis of COAD and improve the detection efficiency of COAD, this paper proposes a multi-level threshold image segmentation (MIS) method based on an enhanced particle swarm algorithm for segmenting COAD images. Firstly, this paper proposes a multi-strategy fusion particle swarm optimization algorithm (DRPSO) with a replacement mechanism. The non-linear inertia weight and sine-cosine learning factors in DRPSO help balance the exploration and exploitation phases of the algorithm. The population reorganization strategy incorporating MGO enhances population diversity and effectively prevents the algorithm from stagnating prematurely. The mutation-based final replacement mechanism enhances the algorithm's ability to escape local optima and helps the algorithm to obtain highly accurate solutions. In addition, comparison experiments on the CEC2020 and CEC2022 test sets show that DRPSO outperforms other state-of-the-art algorithms in terms of convergence accuracy and speed. Secondly, by combining the non-local mean 2D histogram and 2D Renyi entropy, this paper proposes a DRPSO algorithm based MIS method, which is successfully applied to the segments the COAD pathology image problem. The results of segmentation experiments show that the above method obtains relatively higher quality segmented images with superior performance metrics: PSNR = 23.556, SSIM = 0.825, and FSIM = 0.922. In conclusion, the MIS method based on the DRPSO algorithm shows great potential in assisting COAD diagnosis and in pathology image segmentation.

Analysis of Th1/Th2 cytokine and clinical characteristics of patients with head and neck squamous cell carcinoma.

A retrospective analysis was conducted on 58 patients with laryngeal and hypopharyngeal tumors and 27 patients with benign vocal cord lesions to explore the role of serum cytokines in these diseases' characteristics and immunotherapy. The differences in the levels of 12 cytokines were measured. Additionally, the study examined the correlation between T helper cells (Th)1/Th2 cytokine levels and the clinical characteristics and immunotherapy efficacy of laryngeal and hypopharyngeal cancers. The results show that the balance of Th1/Th2 is biased towards Th2 in patients with laryngeal and hypopharyngeal tumors. Among these, interleukin (IL)-6 (P = 0.021) was highly expressed in laryngeal tumors, and the expression levels of IL-1ß (P = 0.008), IL-6 (P = 0.005), and IL-8 (P = 0.05) were higher in patients with poorly differentiated laryngeal tumors. The level of IL-4 (P = 0.0048) was significantly correlated with tumor location. The expression levels of IL-2 (P = 0.010), IL-4 (P = 0.028), IL-10 (P = 0.011), IL-12p70 (P = 0.034), IL-17 (P = 0.024), tumor necrosis factor (TNF)-α (P = 0.003), and interferon (IFN)-γ (P = 0.007) were related to lymph node metastasis. The level of IFN-γ (P = 0.016) was correlated with the efficacy of neoadjuvant therapy, while the level of IFN-α (P = 0.013) was significantly correlated with programmed death ligand 1 (PD-L1) expression. The Principal Component Analysis (PCA) results showed that patients with tumors, poor differentiation, and lymph node metastasis had higher levels of Th1 and Th2 cytokine separation. In conclusion, the shift in the balance of Th1 and Th2 cytokine expression indicates higher tumor invasiveness, and IFN has potential as a circulating molecular marker for immunotherapy of head and neck squamous cell carcinoma.

Integrated Metabolomics and Transcriptomics Analysis Reveals New Insights into Triterpene Biosynthesis in Rosa rugosa.

Rosa rugosa is highly regarded for its aesthetic and therapeutic qualities. In particular, R. rugosa's flowers are known to produce essential oils containing a mixture of volatile terpenes, phenylpropanoids, and other compounds. Despite this, extensive research exists on volatile terpenes in flowers, while the knowledge of non-volatile terpenes in distinct tissues is still limited. Using UPLC-ESI-MS/MS, a comprehensive analysis of the terpene metabolites in five different tissues of R. rugosa was conducted. These metabolites accumulated in distinct tissues, and the majority of them were triterpenoids. Transcriptome data were collected from five tissues using RNA-seq. Transcriptomics and metabolomics were utilized to evaluate the triterpene biosynthesis pathway, resulting in new insights into its regulation and biosynthesis. The RrOSC10 was identified as a key enzyme in converting 2,3-oxidosqualene into α-amyrin, potentially contributing to the triterpene biosynthesis pathway. Furthermore, the expression of the RrOSC10 gene was upregulated by salinity for 0.5 h and 1 h, with subsequent downregulation at 2 h. This study lays a foundation for future research on the biosynthesis and accumulation of triterpenes in R. rugosa.

The GATAD2B-NuRD complex drives DNA:RNA hybrid-dependent chromatin boundary formation upon DNA damage.

Double-strand breaks (DSBs) are the most lethal form of DNA damage. Transcriptional activity at DSBs, as well as transcriptional repression around DSBs, are both required for efficient DNA repair. The chromatin landscape defines and coordinates these two opposing events. However, how the open and condensed chromatin architecture is regulated remains unclear. Here, we show that the GATAD2B-NuRD complex associates with DSBs in a transcription- and DNA:RNA hybrid-dependent manner, to promote histone deacetylation and chromatin condensation. This activity establishes a spatio-temporal boundary between open and closed chromatin, which is necessary for the correct termination of DNA end resection. The lack of the GATAD2B-NuRD complex leads to chromatin hyperrelaxation and extended DNA end resection, resulting in homologous recombination (HR) repair failure. Our results suggest that the GATAD2B-NuRD complex is a key coordinator of the dynamic interplay between transcription and the chromatin landscape, underscoring its biological significance in the RNA-dependent DNA damage response.

Natural pyrethrins induce cytotoxicity in SH-SY5Y cells and neurotoxicity in zebrafish embryos (Danio rerio).

Natural pyrethrins are widely used in agriculture because of their good insecticidal activity. Meanwhile, natural pyrethrins play an important role in the safety evaluation of pyrethroids as precursors for structural development of pyrethroid insecticides. However, there are fewer studies evaluating the neurological safety of natural pyrethrins on non-target organisms. In this study, we used SH-SY5Y cells and zebrafish embryos to explore the neurotoxicity of natural pyrethrins. Natural pyrethrins were able to induce SH-SY5Y cells damage, as evidenced by decreased viability, cycle block, apoptosis and DNA damage. The apoptotic pathway may be related to the involvement of mitochondria and the results showed that natural pyrethrins induced a rise in Capase-3 viability, Ca2+ overload, a decrease in adenosine triphosphate (ATP) and a collapse of mitochondrial membrane potential in SH-SY5Y cells. Natural pyrethrins may mediate DNA damage in SH-SY5Y cells through oxidative stress. The results showed that natural pyrethrins induced an increase in reactive oxygen species (ROS) levels, superoxide dismutase (SOD) activity, malondialdehyde (MDA) content and catalase (CAT) activity, and induced a decrease in glutathione peroxidase (GPx) activity in SH-SY5Y cells. In vivo, natural pyrethrins induced developmental malformations in zebrafish embryos, which were mainly characterized by pericardial edema and yolk sac edema. Meanwhile, the results showed that natural pyrethrins induced damage to the Huc-GFP axis and disturbed lipid metabolism in the head of zebrafish embryos. Further results showed elevated ROS levels and apoptosis in the head of zebrafish embryos, which corroborated with the results of the cell model. Finally, the results of mRNA expression assay of neurodevelopment-related genes indicated that natural pyrethrins exposure interfered with their expression and led to neurodevelopmental damage in zebrafish embryos. Our study may raise concerns about the neurological safety of natural pyrethrins on non-target organisms.

[Research progress on mechanism of traditional Chinese medicine intervention in angiogenesis in prevention and treatment of nontraumatic avascular necrosis of femoral head].

Nontraumatic avascular necrosis of the femoral head(NANFH) is a common and refractory femoral head disease that causes bone death due to interruption of blood supply. Early clinical symptoms are atypical, such as hip pain and limited joint function. In the late stage, severe pain, shortening of the affected limb, claudication, and other serious symptoms are common, which se-riously affects the quality of life of patients. Therefore, it is of great significance to actively improve the clinical symptoms of NANFH to enhance the quality of life of patients. The pathogenesis of NANFH is complex, such as traumatic vascular circulatory disorders, the use of hormones or other drugs, alcoholism, and diabetes mellitus. These factors directly or indirectly lead to femoral head vascular damage, thrombosis, and coagulation system disorders, which reduce the blood supply to the acetabulum and femoral head, thus causing ischaemic death of the femoral head or even femoral head collapse. NANFH is mainly categorized as "bone impotence" and "bone paralysis" in traditional Chinese medicine(TCM). The treatment of NANFH with TCM has the characteristics and advantages of a long history, stable and reliable therapeutic effect, fewer adverse reactions, good patient tolerance, and high acceptance. Previous studies have shown that the promotion of angiogenesis is a key initiative in the prevention and treatment of NANFH, and TCM can promote fe-moral head angiogenesis by interfering with the expression of angiogenesis-related factors, which in turn can help to restore the blood supply of the femoral head and thus improve clinical symptoms of NANFH and prevent and treat NANFH. This article described the roles of blood supply interruption and angiogenesis in NANFH and the accumulated knowledge and experience of TCM in NANFH and summarized the role of angiogenesis-related factors in NANFH and the research progress on TCM intervention, so as to provide an idea for the subsequent research and a new basis for the clinical application of TCM in the treatment of NANFH.

[Effects of humic acid water-soluble fertilizer on growth and physiological characteristics of Bupleurum chinense seedlings].

The effects of humic acid water-soluble fertilizer on the growth and physiological characteristics of Bupleurum chinense seedlings(Zhongchai No.1) were studied by using a single factor experiment design. When the seedling age was 60 days, the humic acid water-soluble fertilizer was diluted 1 200 times(T1), 1 500 times(T2), 1 800 times(T3), and 2 100 times(T4) for seedling treatment, respectively, and water was used as the control(CK). The effects of different treatments on growth indexes, biomass accumulation, root activity, antioxidant enzyme activity, membrane lipid peroxidation, and photosynthetic characteristics of B. chinense seedlings were analyzed after 30 days. The results showed that compared with CK, stem height, leaf number, root diameter, and root length of the B. chinense seedlings under T3 treatment were significantly increased by 36.82%, 37.03%, 42.78%, and 22.38%, respectively. Root fresh weight, leaf fresh weight, root dry weight, and leaf dry weight under T3 treatment were significantly increased by 90.36%, 98.68%, 123.84%, and 104.38%, respectively. In addition, humic acid water-soluble fertilizer also enhanced TTC reducing activity of the root of B. chinense seedlings, inhibited malonaldehyde(MDA) content, increased superoxide dismutase(SOD), peroxidase(POD), and catalase(CAT) enzyme activities, improved chlorophyll content, and enhanced P_n, G_s, T_r, and other photosynthetic parameters. In conclusion, the application of humic acid water-soluble fertilizer diluted 1 800 times can significantly promote the growth of B. chinense seedlings, enhance root vitality, improve seedling stress resistance, and enhance photosynthesis. The results of this study can provide a theoretical basis for fertilization of B. chinense seedlings.

Physical activity, sedentary behavior, and the risk of functional gastrointestinal disorders: A two-sample Mendelian randomization study.

OBJECTIVES: Functional dyspepsia (FD) and irritable bowel syndrome (IBS) are prevalent functional gastrointestinal disorders (FGIDs). In this study we aimed to explore the causal association between physical activity or sedentary behavior and the risk of FD and IBS. METHODS: Mendelian randomization (MR) analysis was employed. Candidate genetic instruments for physical activity and sedentary behavior were retrieved from the latest published Genome-Wide Association Study (GWAS), which included up to 703 901 participants. Summary-level GWAS data for FD (8 875 cases and 320 387 controls) and IBS (9 323 cases and 301 931 controls) were obtained from the FinnGen study. The causal effects were mainly estimated by inverse variance weighted (IVW) method. Sensitivity analyses were implemented with Cochran's Q test, MR-Egger intercept test, leave-one-out analysis, and the funnel plot. RESULTS: No significant association of moderate-to-vigorous intensity physical activity (MVPA), leisure screen time (LST), sedentary behavior at work (SDW), and sedentary commuting (SDC) with the risk of FD was found. However, there was a suggestive correlation between MVPA and the decreased risk of FD (odds ratio [OR] 0.63, 95% confidence interval [CI] 0.39-0.99, P = 0.047). Genetically predicted MVPA decreased the risk of IBS (OR 0.58, 95% CI 0.40-0.84, P = 0.004), while increased LST was positively associated with IBS risk (OR 1.33, 95% CI 1.15-1.53, P < 0.001). No causal effects of SDW or SDC on IBS risk were observed. CONCLUSION: MVPA and LST are causally linked to the development of IBS, which will facilitate primary prevention of IBS.

Does depressurization of the portal vein before liver transplantation affect the recurrence of HCC? A nested case-control study.

BACKGROUND: Portal hypertension (PHT) has been proven to be closely related to the development of hepatocellular carcinoma (HCC). Whether PHT before liver transplantation (LT) will affect the recurrence of HCC is not clear. METHODS: 110 patients with depressurization of the portal vein (DPV) operations (Transjugular Intrahepatic Portosystemic Shunt-TIPS, surgical portosystemic shunt or/and splenectomy) before LT from a HCC LT cohort, matched with 330 preoperative non-DPV patients; this constituted a nested case-control study. Subgroup analysis was based on the order of DPV before or after the occurrence of HCC. RESULTS: The incidence of acute kidney injury and intra-abdominal bleeding after LT in the DPV group was significantly higher than that in non-DPV group. The 5-year survival rates in the DPV and non-DPV group were 83.4% and 82.7% respectively (P = 0.930). In subgroup analysis, patients in the DPV prior to HCC subgroup may have a lower recurrence rate (4.7% vs.16.8%, P = 0.045) and a higher tumor free survival rate (88.9% vs.74.4%, P = 0.044) after LT under the up-to-date TNMI-II stage, while in TNM III stage, there was no difference for DPV prior to HCC subgroup compared with the DPV after HCC subgroup or the non-DPV group. CONCLUSION: Compared with DPV after HCC, DPV treatment before HCC can reduce the recurrence rate of HCC after early transplantation (TNM I-II). DPV before LT can reduce the recurrence of early HCC.

Comprehensive quality evaluation of Lysimachia christinae Hance via fingerprint, spectrum-effect relationship, and quantitative analyses of multiple components by single marker.

BACKGROUND: Lysimachia christinae Hance (LCH) is a traditional medicine used to treat gallstone disease and cholecystitis. Despite its known anti-inflammatory and choleretic effects, its quality has not been extensively evaluated. OBJECTIVE: In this study, we aimed to establish a reliable quality evaluation method for LCH via fingerprint, spectrum-effect relationship, and quantitative analyses of multicomponents by a single marker (QAMS). METHODS: First, the fingerprints and anti-inflammatory and choleretic activities of 14 LCH batches were determined. Then, the gray relation analysis method was used to analyze the peak areas of the fingerprint profile and pharmacodynamic data. Subsequently, the characteristic peaks were tentatively identified using high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Finally, rutin was selected as the internal reference material, and QAMS was used to analyze the LCH components. RESULTS: Pharmacodynamic experiments confirmed that LCH exerted anti-inflammatory and choleretic effects. Moreover, 15 flavonoids related to the anti-inflammatory and choleretic effects of LCH were identified. Notably, relative error percentage between the QAMS and external standard method was less than 5%. CONCLUSION: This study successfully established a comprehensive evaluation method for the qualitative and quantitative analyses of LCH.

VCP/p97 UFMylation stabilizes BECN1 and facilitates the initiation of autophagy.

Macroautophagy/autophagy is essential for the degradation and recycling of cytoplasmic materials. The initiation of this process is determined by phosphatidylinositol-3-kinase (PtdIns3K) complex, which is regulated by factor BECN1 (beclin 1). UFMylation is a novel ubiquitin-like modification that has been demonstrated to modulate several cellular activities. However, the role of UFMylation in regulating autophagy has not been fully elucidated. Here, we found that VCP/p97 is UFMylated on K109 by the E3 UFL1 (UFM1 specific ligase 1) and this modification promotes BECN1 stabilization and assembly of the PtdIns3K complex, suggesting a role for VCP/p97 UFMylation in autophagy initiation. Mechanistically, VCP/p97 UFMylation stabilizes BECN1 through ATXN3 (ataxin 3)-mediated deubiquitination. As a key component of the PtdIns3K complex, stabilized BECN1 facilitates assembly of this complex. Re-expression of VCP/p97, but not the UFMylation-defective mutant, rescued the VCP/p97 depletion-induced increase in MAP1LC3B/LC3B protein expression. We also showed that several pathogenic VCP/p97 mutations identified in a variety of neurological disorders and cancers were associated with reduced UFMylation, thus implicating VCP/p97 UFMylation as a potential therapeutic target for these diseases. Abbreviation: ATG14:autophagy related 14; Baf A1:bafilomycin A1;CMT2Y: Charcot-Marie-Toothdisease, axonal, 2Y; CYB5R3: cytochromeb5 reductase 3; DDRGK1: DDRGK domain containing 1; DMEM:Dulbecco'smodified Eagle's medium;ER:endoplasmic reticulum; FBS:fetalbovine serum;FTDALS6:frontotemporaldementia and/or amyotrophic lateral sclerosis 6; IBMPFD1:inclusion bodymyopathy with early-onset Paget disease with or withoutfrontotemporal dementia 1; LC-MS/MS:liquid chromatography tandem mass spectrometry; MAP1LC3B/LC3B:microtubule associated protein 1 light chain 3 beta; MS: massspectrometry; NPLOC4: NPL4 homolog, ubiquitin recognition factor;PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3;PIK3R4: phosphoinositide-3-kinase regulatory subunit 4; PtdIns3K:phosphatidylinositol 3-kinase; RPL26: ribosomal protein L26; RPN1:ribophorin I; SQSTM1/p62: sequestosome 1; UBA5: ubiquitin likemodifier activating enzyme 5; UFC1: ubiquitin-fold modifierconjugating enzyme 1; UFD1: ubiquitin recognition factor in ERassociated degradation 1; UFL1: UFM1 specific ligase 1; UFM1:ubiquitin fold modifier 1; UFSP2: UFM1 specific peptidase 2; UVRAG:UV radiation resistance associated; VCP/p97: valosin containingprotein; WT: wild-type.