Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing.

MOTIVATION: Advances in whole-genome single-cell DNA sequencing (scDNA-seq) have led to the development of numerous methods for detecting copy number aberrations (CNAs), a key driver of genetic heterogeneity in cancer. While most of these methods are limited to the inference of total copy number, some recent approaches now infer allele-specific CNAs using innovative techniques for estimating allele-frequencies in low coverage scDNA-seq data. However, these existing allele-specific methods are limited in their segmentation strategies, a crucial step in the CNA detection pipeline. RESULTS: We present SEACON (Single-cell Estimation of Allele-specific COpy Numbers), an allele-specific copy number profiler for scDNA-seq data. SEACON uses a Gaussian Mixture Model to identify latent copy number states and breakpoints between contiguous segments across cells, filters the segments for high-quality breakpoints using an ensemble technique, and adopts several strategies for tolerating noisy read-depth and allele frequency measurements. Using a wide array of both real and simulated datasets, we show that SEACON derives accurate copy numbers and surpasses existing approaches under numerous experimental conditions, and identify its strengths and weaknesses. AVAILABILITY AND IMPLEMENTATION: SEACON is implemented in Python and is freely available open-source from https://github.com/NabaviLab/SEACON and https://doi.org/10.5281/zenodo.12727008.

A multimodal graph neural network framework for cancer molecular subtype classification.

BACKGROUND: The recent development of high-throughput sequencing has created a large collection of multi-omics data, which enables researchers to better investigate cancer molecular profiles and cancer taxonomy based on molecular subtypes. Integrating multi-omics data has been proven to be effective for building more precise classification models. Most current multi-omics integrative models use either an early fusion in the form of concatenation or late fusion with a separate feature extractor for each omic, which are mainly based on deep neural networks. Due to the nature of biological systems, graphs are a better structural representation of bio-medical data. Although few graph neural network (GNN) based multi-omics integrative methods have been proposed, they suffer from three common disadvantages. One is most of them use only one type of connection, either inter-omics or intra-omic connection; second, they only consider one kind of GNN layer, either graph convolution network (GCN) or graph attention network (GAT); and third, most of these methods have not been tested on a more complex classification task, such as cancer molecular subtypes. RESULTS: In this study, we propose a novel end-to-end multi-omics GNN framework for accurate and robust cancer subtype classification. The proposed model utilizes multi-omics data in the form of heterogeneous multi-layer graphs, which combine both inter-omics and intra-omic connections from established biological knowledge. The proposed model incorporates learned graph features and global genome features for accurate classification. We tested the proposed model on the Cancer Genome Atlas (TCGA) Pan-cancer dataset and TCGA breast invasive carcinoma (BRCA) dataset for molecular subtype and cancer subtype classification, respectively. The proposed model shows superior performance compared to four current state-of-the-art baseline models in terms of accuracy, F1 score, precision, and recall. The comparative analysis of GAT-based models and GCN-based models reveals that GAT-based models are preferred for smaller graphs with less information and GCN-based models are preferred for larger graphs with extra information.

Sleeve gastrectomy decreased hepatic lipid accumulation by inducing autophagy via AMPK/mTOR pathway.

This study was designed to investigate the roles of autophagy in the attenuation of hepatic lipid accumulation after sleeve gastrectomy (SG). Thirty-two rats were divided into normal control, obesity group, sham group, and SG group. Then serum glucagon-like polypeptide-1 (GLP-1) and lipid accumulation were determined, followed by measuring the activity of autophagy based on immunohistochemistry (IHC) and Western blot analysis. Our data showed significant decrease in the lipid accumulation after SG compared with sham group. GLP-1 and autophagy showed significant increase in rats underwent SG compared with the sham group (P < 0.05). In vitro experiments were conducted to analyze the roles of GLP-1 in autophagy. We knock-downed the expression of Beclin-1 in HepG2, and then analyzed the expression of autophagy-related protein (i.e. LC3BII and LC3BI) and lipid droplet accumulation. In HepG2 cells, GLP-1 analog reduced lipid accumulation by activating autophagy through modulating the AMPK/mTOR signaling pathway. All these concluded that SG decreased hepatic lipid accumulation by inducing autophagy through modulating AMPK/mTOR pathway.

The influence of three antibiotics on the growth, intestinal enzyme activities, and immune response of the juvenile sea cucumber Apostichopus japonicus selenka.

The global abuse and misuse of antibiotics in the treatment and prevention of bacterial infections has resulted in the ubiquitous existence of these drugs in aquatic environments, which causes frequent antimicrobial resistance and pollution in ecosystems. However, the chronic effects of antimicrobial agents on aquatic animal growth and health have not been fully evaluated. In the present study, three typical antibiotics (tetracycline, erythromycin, and norfloxacin) were administered orally to juvenile sea cucumbers Apostichopus japonicus for 45 days, to mimic the long-term use of antibiotics. As a result, tetracycline and erythromycin promoted the growth and digestive activity of lipase, pepsin, and trypsin, but norfloxacin did not show significant prompting effect on digestive activity and even retarded the weight gain of the sea cucumbers. The mortality was higher in antibiotic treated groups between the 2nd and 4th days after challenge with Vibrio splendidus. At the same time, lower immune-related parameters were found in antibiotic feeding juveniles, suggesting that the use of antibiotics might weaken the immune defense system of sea cucumbers. This study revealed that antibiotic administration could facilitate the growth of sea cucumbers to varying degrees yet coupled with high risks of impaired immune function and compromised disease resistance.

The effects of benzo[a]pyrene on the composition of gut microbiota and the gut health of the juvenile sea cucumber Apostichopus japonicus Selenka.

The gut microbiota is essential for health and physiological functions in the host organism. However, the toxicological evaluation of environmental pollutants on the gut microbiota is still insufficient. In the present study, the juvenile sea cucumber Apostichopus japonicus was exposed for 14 days to Benzo[a]pyrene (BaP), which is a model polycyclic aromatic hydrocarbon (PAH), at four different concentrations (0, 0.5, 5, and 25 µg/L). We analyzed the intestinal microbial community of A. japonicas using 16S rRNA gene amplicon sequencing. Our results demonstrate that BaP exposure caused alterations to the microbiome community composition in sea cucumbers. At the phylum level, Planctomycetes were significantly more abundant in BaP exposure groups at 14 d compared with the control group, and the abundance of Proteobacteria and Bacteroidetes increased while the abundance of Firmicutes decreased following BaP exposure. At the genus level, multiple beneficial and autochthonous genera declined in the BaP treatment groups compared to the control, including Lactococcus, Bacillus, Lactobacillus, Enterococcus, Leuconostoc and Weissella; however, a bloom of alkane-degrading bacteria was found in BaP-exposed guts and included Lutibacter, Pseudoalteromonas, Polaribacter, Rhodopirellula and Blastopirellula. Furthermore, histological morphology, enzymatic activity and gene expression analysis revealed that BaP exposure also negatively impacted gut structure and function and presented as inflammation or atrophy, oxidative stress and immune suppression in sea cucumber intestines. Collectively, these findings provide insights into the toxic effects of BaP exposure on A. japonicas associated with intestinal microbiota and health.

Overexpression and purification of HSV-2 glycoprotein D in suspension CHO cells with serum-free medium and immunogenicity analysis.

Glycoprotein D (gD2) is the most important candidate antigen for herpes simplex virus type 2 (HSV-2) vaccine development. Establishment of a stable eukaryotic cell line to overexpress gD2 and an efficient purification process to purify is essential for the development of subunit vaccine against HSV-2. The DNA sequence of the extracellular epitope-rich fragment of gD2 was optimized, chemically synthesized, and cloned into plasmid pMD902. The recombinant plasmid pMD902-gD was stably transfected into CHO-DG44 cells, and cell lines with high levels of expression of gD2 were established. The recombinant gD2 was purified efficiently using an anion exchange column and a Sephadex G-25 desalting column. The yield of the purified gD2 was 57 mg/L of serum-free culture medium, and its purity was determined to be about 95% by HPLC analysis. Finally, the immunogenicity of the purified gD2 was measured and it induced strong and specific humoral immunity and higher level of cellular immune response than gD2 expressed in prokaryotic cells. We established a stable, secretory, and high-yield gD2-expression cell line and an easy and efficient gD2-purification process, which lays the foundation for preparation of large amount of gD2 that is essential for HSV-2 subunit vaccine development.

Safety assessment of sand casting explosion accidents by testing cavity pressure of the sand mold to protect employee health.

Excessive cavity pressure may result in a sand casting explosion, and corresponding measures should be adopted to prevent these consequences. In this study, the pressure variations in the cavity were first investigated based upon on-site testing by taking the resin contents into consideration, and then the evolution characteristics of sand casting explosion accidents were analyzed in depth by system dynamics, chaos theory, and the bow-tie model. When the resin contents are 1.3 wt%, 1.4 wt%, and 1.5 wt%, the pressures of the gas vent increase by 27.0 Pa, 32.8 Pa, and 35.6 Pa, respectively. To reduce the pressure of the cavity, the resin content should be reduced. The evolutionary process of sand casting explosion accidents has a noticeable butterfly effect and randomness, whose occurrence is comprehensively affected by human, object, environment, management and emergency subsystems. The leading causes of sand casting explosion accidents mainly include the extensive gas evolution characteristics of foundry sand, cavity exhaust blockage, and inadequate safety monitoring. The leading consequences of sand casting explosion accidents mainly include casualties, secondary disasters, and social panic. The implications of these findings concerning sand casting explosion accidents can be regarded as the foundation for accident prevention in practice.

Variation in Nitrogen Utilization and Nutrient Composition across Various Organs under Different Strip Logging Management Models in Moso Bamboo (Phyllostachys edulis) Forest.

The rapid restoration and renewal of the moso bamboo logging zone after strip logging has emerged as a key research area, particularly regarding whether nutrient accumulation and utilization in reserve zones can aid in the restoration and regeneration of the logging zone. In this study, a dynamic 15N isotope tracking experiment was conducted by injecting labeled urea fertilizer into bamboo culms. Logging zones and reserve zones of 6 m, 8 m, and 10 m widths were established. The conventional selective logging treatment served as a control (Con). Measurements were taken in May and October to assess the differences in nitrogen accumulation ability, utilization rates, and nutrient content across different organs in bamboo forests at different growth stages and under different treatments. Principal component analysis was conducted to evaluate and determine the importance of each indicator and strip logging treatment comprehensively. The results showed that various bamboo organs exhibited higher nitrogen accumulation and utilization rates during the peak growth period compared to the late growth period. Leaves had the highest nitrogen accumulation and utilization rates than the other organs. The average C content in various bamboo organs under different logging treatments exhibited subtle differences, irrespective of variation in logging width treatments. Bamboo culm exhibited the highest carbon accumulation. The C content in various bamboo organs was higher during the peak growth period than in the late growth period. The nitrogen content peaked in the leaves during the two growth stages and was significantly higher compared to the other organs. Most bamboo organs in the logging zones exhibited relatively higher nitrogen content than in the reserve zone and Con group. The P content was highest in bamboo leaves compared with other organs across the different strip logging treatments. Principal component analysis revealed relatively high absolute values of the coefficients for the C content, bamboo stump C content, and culm Ndff%. Log8 and Res10 zones had the highest comprehensive evaluation scores, indicating that Log8 and Res10 had the best effect on the promotion of nitrogen utilization and nutrient accumulation in various organs of moso bamboo.

Transcriptomic and Phenotypical Analysis of the Physiological Plasticity of Chamaecyparis hodginsii Roots under Different Nutrient Environments and Adjacent Plant Competition.

Chamaecyparis hodginsii seedlings undergo significant changes during growth due to different nutrient environments and adjacent plant competition, which is evident in the physiological plasticity changes in their roots. Therefore, in this experiment, 20 one-year-old elite C. hodginsii family seedlings were selected as the test objects, and the different nutrient environments and adjacent plant competition environments in nature were artificially simulated. Four nutrient environments (N heterogeneous nutrient environment, P heterogeneous nutrient environment, K heterogeneous nutrient environment, and homogeneous environment) and three planting patterns (single plant, conspecific neighbor, and heterospecific neighbor) were set up to determine the differences in root physiological indexes and plasticity of different family seedlings, and the families and treatment combinations with higher comprehensive evaluation were selected. The transcriptome sequencing of fine roots of C. hodginsii under different treatments was performed to analyze the differentially expressed genes. The results showed that the root activity, antioxidant enzyme activity, and nutrient element content of C. hodginsii seedlings in the N and P heterogeneous environments were higher than those in the homogeneous nutrient environment, while there was no significant difference between the K heterogeneous nutrient environment and the homogeneous environment, but MDA content was higher than that in other nutrient environments. The root activity and antioxidant enzyme activity in the competitive patterns were generally higher than those in the single plant and reached the peak in the heterospecific neighbor. The root physiological plasticity index of line 490 was the highest, but the comprehensive evaluation of root physiological indexes of lines 539 and 535 was better. The pattern with the highest comprehensive evaluation score was P heterogeneous nutrient environment × heterospecific neighbor. The effects of the N and P heterogeneous nutrient environments on root transcriptome genes were similar, which significantly increased DNA transcription and regulatory factor activity, while K heterogeneous nutrient environment focused on the regulation of root enzyme activity. The heterogeneous nutrient environment induces the conduction of hormone signals in the roots of C. hodginsii and induces the synthesis of phenylpropanone. The biosynthesis of phenylpropanone in the roots of C. hodginsii will increase significantly under competitive patterns. In summary, the N and P heterogeneous nutrient environments and the heterospecific neighbor can improve the root physiological indexes of C. hodginsii families, and the root physiological indexes of lines 539 and 535 are the best. The nutrient environment and competition pattern mainly affect the root system to transmit hormone signals to regulate enzyme activity.

Gentiopicroside inhibits the progression of gastric cancer through modulating EGFR/PI3K/AKT signaling pathway.

BACKGROUND: This study was designed to clarify the function and potential mechanism of gentiopicroside (GPS) in regulating the malignant progression of gastric cancer (GC) through in vitro cellular experiments and in vivo animal models. METHODS: AGS and HGC27 cells were divided into control group and GPS treatment groups (50 µM and 100 µM). Then, the cellular proliferation, colony formation, migration, invasion, and apoptosis were detected, respectively. Transmission electron microscope (TEM) was used to observe the mitochondrial changes, and the mitochondrial membrane potential (MMP) was determined using the JC-1 commercial kit. Network pharmacology analysis was utilized to screen the potential molecule that may be related to the GPS activity on GC cells, followed by validation tests using Western blot in the presence of specific activator. In addition, xenografted tumor model was established using BALB/c nude mice via subcutaneous injection of HGC27 cells, along with pulmonary metastasis model. Then, the potential effects of GPS on the tumor growth and metastasis were detected by immunohistochemistry (IHC) and HE staining. RESULTS: GPS inhibited the proliferation, invasion and migration of GC cell lines in a dose-dependent manner. Besides, it could induce mitochondrial apoptosis. Epidermal growth factor receptor (EGFR) may be a potential target for GPS action in GC by network pharmacological analysis. GPS inhibits activation of the EGFR/PI3K/AKT axis by reducing EGFR expression. In vivo experiments indicated that GPS induced significant decrease in tumor volume, and it also inhibited the pulmonary metastasis. For the safety concerns, GPS caused no obvious toxicities to the heart, liver, spleen, lung and kidney tissues. IHC staining confirmed GPS downregulated the activity of EGFR/PI3K/AKT. CONCLUSIONS: Our investigation demonstrated for the first time that GPS could inhibit GC malignant progression by targeting the EGFR/PI3K/AKT signaling pathway. This study indicated that GPS may be serve as a safe anti-tumor drug for further treatment of GC.