Cloning and expression analysis of superoxide dismutase SmMSD2 gene from Salvia miltiorrhiza / 药学学报

Superoxide dismutase (SOD) is a key enzyme that scavenge superoxide anion free radical (O2·-) in vivo, and plays an important role in plant growth and development and stress. In this study, according to the genome and transcriptome data of Salvia miltiorrhizae, 9 SOD genes were identified and the expression patterns of SOD family genes were further analyzed, including 5 Cu/Zn-SOD, 2 Fe-SOD and 2 Mn-SOD. On the basis of proteomic analysis, combined with transcriptome data, one full-length cDNA of Mn-SOD gene, namely SmMSD2 was cloned from Salvia miltiorrhizae. The results of amino acid sequence alignment and phylogenetic analysis showed that SmMSD2 protein belongs to the manganese superoxide dismutase (Mn-SOD) subfamily, and SmMSD2 protein shares high sequence identity with the Mn-SOD proteins of various plants that all contain a C-terminal conserved metal-binding domain "DVWEHAYY". The prokaryotic expression vector pMAL-c2X-SmMSD2 was constructed and transformed into E. coli BL21 expressing strain, and the target recombinant protein was successfully induced and its enzymatic properties were analyzed. Spatiotemporal expression analysis showed that SmMSD2 gene was expressed in all tissues, indicating that SmMSD2 gene was constitutively expressed at a stable level. Real-time quantitative PCR indicated that drought (15% PEG6000), abscisic acid (ABA) and indole-3-acetic acid (IAA) could induce the expression of SmMSD2 gene, suggesting that SmMSD2 may be involved in the response of Salvia miltiorrhizae to abiotic stress such as drought, as well as the signaling pathways of phytohormone ABA and IAA. These results lay the foundation for further elucidating the involvement of superoxide dismutase in the stress response and accumulation of active components of Salvia miltiorrhiza.

Exploration on "Efficacy-toxicity" Association Mechanisms of Tripterygium wilfordii Polyglycoside Tablets Against Rheumatoid Arthritis Based on Multi-omics Integrated Regulatory Network / 中国实验方剂学杂志

ObjectiveTo explore the "efficacy-toxicity" association mechanisms of Tripterygium wilfordii polyglycoside tablets （TWPT） by establishing and analyzing an interaction network associated with the clinical efficacy of TWPT in the treatment of rheumatoid arthritis （RA） and TWPT-induced liver injury. MethodOn the basis of the TWPT efficacy-related gene expression profile and TWPT-induced liver injury-related protein expression profile which were both obtained from our clinical cohorts， the "efficacy-toxicity" association network of TWPT was constructed， and the key network targets were identified by calculating the topological values of the nodes， including the degree， closeness and betweenness. After that， the biological functions and pathways of the key network targets were investigated by enrichment analysis. ResultA total of 119 differentially expressed genes （58 up-regulated and 61 down-regulated） between RA patients with TWPT well and weak response were identified as TWPT efficacy-related genes by clinical transcriptomics， and 49 differentially expressed proteins （36 up-regulated and 13 down-regulated） were demonstrated to be TWPT-induced liver injury-related proteins by clinical proteomics. In addition， the clinical symptom enrichment analysis indicated that the TWPT efficacy-related genes were significantly associated with various clinical symptoms of arthralgia in traditional Chinese medicine and clinical phenotypes of modern medicine， and most of the TWPT-induced liver injury-related proteins were involved in digestive system abnormalities. Therefore， the aforementioned multi-omics data represented the main clinical symptoms of TWPT treating RA and inducing liver injury. Mechanically， the "efficacy-toxicity" association network revealed that both TWPT efficacy-related genes and TWPT-induced liver injury-related core proteins were involved in the "immune-inflammatory" imbalance， especially playing an important role in neutrophil degranulation， complement cascade reaction， and immune-inflammatory response mediated by protein post-translational modification. Notably， the above genes and proteins were also enriched in various signaling pathways related to cell proliferation and cell cycle regulation， such as RAS and mitogen-activated protein kinase （MAPK） signaling pathway， and in several liver functional processes， such as glycogen metabolism and redox reaction. ConclusionThis study systematically explained the "efficacy-toxicity" association characteristics and molecular mechanisms of TWPT by applying a research strategy integrating clinical phenomics， transcriptomics and proteomics， laying a good data foundation for exploring the "efficacy enhancing and toxicity-reducing" mechanisms of TWPT.

Advances in research methods for biosynthetic pathway analysis of active ingredients in traditional Chinese medicine / 中国中药杂志

The active ingredients in traditional Chinese medicine(TCM)are the foundation for the efficiency of TCM and the key to the formation of Dao-di herbs. It is of great significance to study the biosynthesis and regulation mechanisms of these active ingredients for analyzing the formation mechanism of Daodi herbs and providing components for the production of active ingredients in TCM by synthetic biology. With the advancements in omics technology, molecular biology, synthetic biology, artificial intelligence, etc., the analysis of biosynthetic pathways for active ingredients in TCM is rapidly progressing. New methods and technologies have promoted the analysis of the synthetic pathways of active ingredients in TCM and have also made this area a hot topic in molecular pharmacognosy. Many researchers have made significant progress in analyzing the biosynthetic pathways of active ingredients in TCM such as Panax ginseng, Salvia miltiorrhiza, Glycyrrhiza uralensis, and Tripterygium wilfordii. This paper systematically reviewed current research me-thods for analyzing the biosynthetic functional genes of active ingredients in TCM, elaborated the mining of gene elements based on multiomics technology and the verification of gene functions in plants in vitro and in vivo with candidate genes as objects. Additionally, the paper summarized new technologies and methods that have emerged in recent years, such as high-throughput screening, molecular probes, genome-wide association studies, cell-free systems, and computer simulation screening to provide a comprehensive reference for the analysis of the biosynthetic pathways of active ingredients in TCM.

The role and regulatory mechanism of tissue and organ crosstalk on skeletal muscle development: a review / 生物工程学报

Skeletal muscle is one of the most important organs in animal, and the regulatory mechanism of skeletal muscle development is of great importance for the diagnosis of muscle-related diseases and the improvement of meat quality of livestock. The regulation of skeletal muscle development is a complex process, which is regulated by a large number of muscle secretory factors and signaling pathways. In addition, in order to maintain steady-state and maximum use of energy metabolism in the body, the body coordinates multiple tissues and organs to form the complex and sophisticated metabolic regulation network, which plays an important role for the regulation of skeletal muscle development. With the development of omics technologies, the underlying mechanism of tissue and organ communication has been deeply studied. This paper reviews the effects of crosstalk among adipose tissue, nerve tissue and intestinal tissue on skeletal muscle development, with the aim to provide a theoretical basis for targeted regulation of skeletal muscle development.

Network pharmacology approaches for research of Traditional Chinese Medicines / 中国天然药物

Pharmacodynamics material basis and effective mechanisms are the two main issues to decipher the mechnisms of action of Traditional Chinese medicines (TCMs) for the treatment of diseases. TCMs, in "multi-component, multi-target, multi-pathway" paradigm, show satisfactory clinical results in complex diseases. New ideas and methods are urgently needed to explain the complex interactions between TCMs and diseases. Network pharmacology (NP) provides a novel paradigm to uncover and visualize the underlying interaction networks of TCMs against multifactorial diseases. The development and application of NP has promoted the safety, efficacy, and mechanism investigations of TCMs, which then reinforces the credibility and popularity of TCMs. The current organ-centricity of medicine and the "one disease-one target-one drug" dogma obstruct the understanding of complex diseases and the development of effective drugs. Therefore, more attentions should be paid to shift from "phenotype and symptom" to "endotype and cause" in understanding and redefining current diseases. In the past two decades, with the advent of advanced and intelligent technologies (such as metabolomics, proteomics, transcriptomics, single-cell omics, and artificial intelligence), NP has been improved and deeply implemented, and presented its great value and potential as the next drug-discovery paradigm. NP is developed to cure causal mechanisms instead of treating symptoms. This review briefly summarizes the recent research progress on NP application in TCMs for efficacy research, mechanism elucidation, target prediction, safety evaluation, drug repurposing, and drug design.

Spatially resolved expression landscape and gene-regulatory network of human gastric corpus epithelium

Molecular knowledge of human gastric corpus epithelium remains incomplete. Here, by integrated analyses using single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) techniques, we uncovered the spatially resolved expression landscape and gene-regulatory network of human gastric corpus epithelium. Specifically, we identified a stem/progenitor cell population in the isthmus of human gastric corpus, where EGF and WNT signaling pathways were activated. Meanwhile, LGR4, but not LGR5, was responsible for the activation of WNT signaling pathway. Importantly, FABP5 and NME1 were identified and validated as crucial for both normal gastric stem/progenitor cells and gastric cancer cells. Finally, we explored the epigenetic regulation of critical genes for gastric corpus epithelium at chromatin state level, and identified several important cell-type-specific transcription factors. In summary, our work provides novel insights to systematically understand the cellular diversity and homeostasis of human gastric corpus epithelium in vivo.

Application of emerging technologies for gut microbiome research

Microbiome is associated with a wide range of diseases. The gut microbiome is also a dynamic reflection of health status, which can be modified, thus representing great potential to exploit the mechanisms that influence human physiology. Recent years have seen a dramatic rise in gut microbiome studies, which has been enabled by the rapidly evolving high-throughput sequencing methods (i.e. 16S rRNA sequencing and shotgun sequencing). As the emerging technologies for microbiome research continue to evolve (i.e. metatranscriptomics, metabolomics, culturomics, synthetic biology), microbiome research has moved beyond phylogenetic descriptions and towards mechanistic analyses. In this review, we highlight different approaches to study the microbiome, in particular, the current limitations and future promise of these techniques. This review aims to provide clinicians with a framework for studying the microbiome, as well as to accelerate the adoption of these techniques in clinical practice.

Advancements in artificial intelligence and machine learning in revolutionising biomarker discovery

Abstract The article explores the significance of biomarkers in clinical research and the advantages of utilizing artificial intelligence (AI) and machine learning (ML) in the discovery process. Biomarkers provide a more comprehensive understanding of disease progression and response to therapy compared to traditional indicators. AI and ML offer a new approach to biomarker discovery, leveraging large amounts of data to identify patterns and optimize existing biomarkers. Additionally, the article touches on the emergence of digital biomarkers, which use technology to assess an individual's physiological and behavioural states, and the importance of properly processing omics and multi-omics data for efficient handling by computer systems. However, the article acknowledges the challenges posed by AI/ML in the identification of biomarkers, including potential biases in the data and the need for diversity in data representation. To address these challenges, the article suggests the importance of regulation and diversity in the development of AI/ML algorithms.

Research progress of artificial intelligence combined with omics data in the diagnosis and treatment of non-small cell lung cancer / 中国胸心血管外科临床杂志

@#In recent years, the computer science represented by artificial intelligence and high-throughput sequencing technology represented by omics play a significant role in the medical field. This paper reviews the research progress of the application of artificial intelligence combined with omics data analysis in the diagnosis and treatment of non-small cell lung cancer (NSCLC), aiming to provide ideas for the development of a more effective artificial intelligence algorithm, and improve the diagnosis rate and prognosis of patients with early NSCLC through a non-invasive way.

Immune-related Features of Esophageal Squamous Cell Carcinoma：A Multi-omics Perspective / 中山大学学报(医学科学版)

Esophageal squamous cell carcinoma is a common malignancy in the Asia-Pacific region， especially in China， where the morbidity remains high in spite of the improved overall survival due to advances in medical technology. Immunotherapy becomes a hot spot in recent tumor research when it has provided significant survival benefits in patients with advanced malignant tumors， such as lung cancer， breast cancer， colon cancer， etc. In esophageal squamous cell carcinoma， immunotherapy promotes survival benefit as well. However， because of the complex and changeable biological functions and gene expression regulation of malignant tumors， the conclusions based on a single-omics analysis are often incomprehensive. Currently， most of the immune-related studies on esophageal squamous cell carcinoma are still confined to a single-omics study like genomics， with limitations and one-sidedness. Since multi-omics analysis helps us better understand tumors from a wider and deeper perspective， this review explores and summarizes immune-related features of esophageal squamous cell carcinoma from a multi-omics perspective.

Microfluidic chip and mass spectrometry-based detection of bacterial antimicrobial resistance and study of antimicrobial resistance mechanism / 中国药科大学学报

@#Bacterial antimicrobial resistance (AMR) is a globally serious problem that threatens public health security.Misuse and abuse of antibiotics cannot achieve the effect of treating bacterial infectious diseases, but will trigger the SOS response of bacteria, exacerbating the evolution of bacterial AMR and the spread of resistant bacteria.This article focuses on antibiotic-resistant bacteria, briefly introduces the pathogenesis of bacterial AMR and SOS response, and systematically summarizes the determination and mechanism study of bacterial AMR based on microfluidics and mass spectrometry.This article provides theoretical basis for AMR-related drug target mining and new drug development, aiming to develop new methods for rapid detection of bacterial AMR and new methods for bacteria inhibition, and promote the diagnosis and treatment of clinical bacteria infectious diseases.

Progress in detection methods for urogenital Chlamydia trachomatis infection / 中华微生物学和免疫学杂志

Urogenital Chlamydia trachomatis ( Ct) infection is a serious sexually transmitted disease worldwide. The early diagnosis and treatment of Ct infection is critical for disease control. This review summarized the progress in the development of methods for detecting Ct infection and discussed the advantages and disadvantages of various methods. The emerging omics techniques in recent years are expected to be new tools for the detection of Ct infection. It is necessary to develop the omics techniques into rapid and accurate point-of-care tests that can be carried out in various testing environments for more effective patient management and disease control.

Prediction of myometrial invasion of bladder cancer based on texture analysis of the bladder wall at tumor base / 中华超声影像学杂志

Objective:To identify the value of ultrasound radiomic features extracted from the bladder wall at tumor base in predicting myometrial invasion of bladder cancer.Methods:A total of 175 cases with bladder cancer confirmed by pathology from January 2017 to February 2022 in the First Affiliated Hospital of Guangxi Medical University were retrospectively analyzed. They were divided into training set and testing set in a ratio of 7∶3. The MaZda texture analysis software was used to draw the region of interest (ROI) of the bladder wall and the tumor region for extracting texture features. The minimum absolute reduction and variable selection operator (LASSO) regression and 10-fold cross-validation were used to screen the features of training set for establishing the models. And the ROC curve was used to evaluate the efficiency of the models.Results:A total of 279 texture features were extracted from the ROI of the bladder wall and the tumor region, and 5 texture features were screened out for constructing omics scoring models by LASSO regression and 10-fold cross-test. The area under ROC curve (AUC)s used in training set and testing set of the bladder wall were 0.921 and 0.856, while the AUCs applied in training set and testing set of the tumor region were 0.849 and 0.704. Both in the training set and test set, the AUCs of the model of the bladder wall were higher than those of the model of the tumor region (all P<0.05). Conclusions:The omics scoring model based on the texture features of the bladder wall at tumor base can effectively identify muscle-invasive bladder cancer(MIBC) and non-muscle-invasive bladder cancer(NMIBC), and has better performance than the model based on the texture feature of the tumor region.

Toward precision medicine: Prospect of asthma diagnosis related technology / 中国综合临床

Bronchial asthma is a heterogeneous disease characterized by chronic airway inflammation. In recent years, the diagnosis and treatment of asthma tend to be precision medicine, and the individualized treatment of asthma is mainly based on individualized diagnosis. However, the pathogenesis of asthma is complex and the clinical phenotype is different, and its high heterogeneity also brings great challenges to realize individualized diagnosis and treatment, Diagnosis and evaluation based on multi-dimensional and multi-means is an important practical development direction.

Phosphoproteomic analysis of human umbilical venous endothelial cells with DENV-2 infection / 南方医科大学学报

OBJECTIVE@#To analyze the differentially phosphorylated proteins in DENV-2-infected human umbilical venous endothelial cells (HUVECs) and explore the possible pathogenic mechanism of DENV-2 infection.@*METHODS@#The total proteins were extracted from DENV-2-infected HUVECs and blank control HUVEC using SDT lysis method. The phosphorylated proteins were qualitatively and quantitatively analyzed using tandem mass spectrometry (TMT). The identified differentially phosphorylated proteins were analyzed by bioinformatics analyses such as subcellular localization analysis, GO enrichment analysis, KEGG pathway analysis and protein-protein interaction (PPI) analysis. Western blotting was used to detect the expressions of phosphorylated Jun, map2k2 and AKT1 proteins in DENV-2-infected HUVECs.@*RESULTS@#A total of 2918 modified peptides on 1385 different proteins were detected, and among them 1346 were significantly upregulated (FC > 1.2, P < 0.05) and 1572 were significantly downregulated (FC < 0.83, P < 0.05). A total of 49 phosphorylated conserved motifs were obtained by amino acid conservative motif analysis. The most abundant differentially phosphorylated peptides in protein domain analysis included RNA recognition motif, protein kinase domain and PH domain. Subcellular localization analysis showed that the differentially modified peptides were mainly localized in the nucleus and cytoplasm. GO enrichment and KEGG pathway analysis showed that the differential peptides were mainly enriched in the regulation of stimulation response, biosynthesis of small molecules containing nuclear bases, and migration of phagosomes and leukocytes across the endothelium. PPI and KEGG joint analysis showed that the up-regulated and down-regulated differentially phosphorylated proteins were enriched in 15 pathways. In DENV-2-infected HUVECs, Western blotting detected differential expressions of phosphorylated proteins related with the autophagy pathway, namely JUN, MAP2K2 and AKT1, and among them p-JUN was significantly down-regulated and p-AKT1 and p-MAP2K2 were significantly upregulated (P < 0.01).@*CONCLUSION@#DENV-2 infected HUVECs show numerous differentially expressed proteins. The downregulation of p-JUN and upregulation of p-MAP2K2 and p-AKT1 suggest their potential roles in regulating autophagy, which is probably involved in the mechanism of DENV-2 infection.

Achievements of agricultural biotechnology: An initiative to double the farmer’s income through cutting edge technology

The population of the world is increasing nearly exponentially over time. To feed this population following the environment conservation protocol, it is essential to enhance the agricultural productivity even in the synchronizing agrarian land use pattern. To enhance the quality and productivity in agriculture sector, introducing the cutting edge technology is need of the hour.From ancient times, traditional approaches like selective breeding, adoption of agronomic management practices and application of indigenous technical knowledge have been used to attain resilience against various abiotic and biotic stresses. However, these traditional approaches are not sufficient to tackle the increasing repercussions of climate change and feed quality food to the expanding population. Therefore, in order to address these issues of climate change, population explosion and malnutrition, biotechnological interventions can be a promising approach. In the past, biotechnology based approaches have given successful products like Herbicide-resistant Soybean, Pusa Basmati 1, Bt Cotton, Bt Brinjal, Flavr-Savr tomato, a therapeutically significant product of Lithospermum erythrorhizon and Panax ginseng. Besides that many more need based products are in pipeline which is under scrutiny of regulatory bodies, policymakers and environmentalists. It is profoundly expected that in the coming day’s agricultural biotechnology applications will bring revolutionary changes to existing agricultural scenario. Therefore, in this review, we have summarized the achievement of agricultural biotechnology that is assisting to enhance the agricultural produce to double the income of farmers. However, this much is not enough; hence full utilization of all the sustainable agricultural biotechnological tools must come into the existence that definitely will boost the agricultural productivity.

Novel biomarkers of sepsis-associated acute respiratory distress syndrome / 中国小儿急救医学

Acute respiratory distress syndrome(ARDS)is one of the most common complications of sepsis, resulting in the high risk of death in patients with sepsis.By comparison with non-septic ARDS, sepsis-associated ARDS is characterized by high morbidity, heterogeneity and mortality.It is vital to early identify the occurrence of ARDS, accurately assess the severity, as well as effectively implement the individualized treatment.Based on the genome-wide association study, mass cytometry, and multiple omics data analysis, the molecular signatures of sepsis-associated ARDS have been elucidated, which were related to genetic susceptibility, inflammatory reaction pathway, and metabolic characteristics.The development of novel biomarkers is helpful to molecular classifier, risk stratification, early recognition and assessing severity, implement early intervention, then improving the prognosis.

Application Prospect of Integrative Omics in Forensic Identification of Methamphetamine-Associated Psychosis / 法医学杂志

The clinical symptoms and signs of methamphetamine-associated psychosis (MAP) and schizophrenia are highly similar, but the situation is completely different when MAP and schizophrenia patients need to be assessed for criminal responsibility after they comitted a harmful behavior. Therefore, the distinction between the two psychoses is very important in forensic psychiatry. At present, the identification of these two psychoses is mainly dependent on the corresponding criteria such as the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) and the Chinese Classification of Mental Disorders Version 3 (CCMD-3). It's challenging to diagnose and distinguish between the two in practical cases due to their similar clinical symptoms and the lack of effective objective indexes. Different from the limitations of single omics, integrative omics intergrates data from multiple dimensions and has been extensively studied in the field of schizophrenia and has achieved some preliminary results. In view of the correlation between MAP and schizophrenia and the potential application value of integrative omics, this paper proposes an integrative omics strategy for MAP pathogenesis and forensic identification, aiming to improve the further understanding of the relationship between the two psychoses and the corresponding pathogenesis. It also provides references for the future exploration of integrative omics in forensic precise identification and effective monitoring and early warning methods.

Twenty years in the 21st century: research approaches and techniques in modern system biology for mechanisms of Chinese medicinal processing / 中国中药杂志

Clarifying the mechanisms of Chinese medicinal processing is pivotal to the modernization of Chinese medicine. Research on Chinese medicinal processing gives priority to the mechanisms of the processing in enhancing efficacy, reducing toxicity, and repurposing medicinals. During the past 20 years, scholars have carried out in-depth studies on the mechanisms of Chinese medicinal processing via modern system biology. They mainly focused on the changes of medicinal properties and efficacy caused by processing using techniques of modern pharmacology and molecular biology, spectrum-efficacy correlation, and biophoton emission. However, these techniques fail to reflect the holistic view of traditional Chinese medicine. With the introduction of system biology, multi-omics techno-logies(genomics, transcriptomics, proteomics, and metabolomics) have surged, which have been applied to the research on the mec-hanisms of Chinese medicinal processing. These multi-omics technologies have advantages in the research on holism. This study aims to summarize the research techniques and approaches in system biology for mechanisms of Chinese medicinal processing in the past 20 years and analyze the limitations and advantages of them. It is concluded that the multi-omics techniques of system biology can reconstruct the mechanisms of Chinese medicinal processing. This study provides a new direction for further research on the mechanisms of Chinese medicinal processing.

Using OMICS technologies to analyze the mechanisms of synthetic microbial co-culture systems: a review / 生物工程学报

In recent years, the interaction mechanisms underpinning the synthetic microbial co-culture systems have gained increasing attention due to their potentials in various biotechnological applications. Exploration of the inter-species mechanisms underpinning the synthetic microbial co-culture system could contribute to a better understanding of the theoretical basis to further optimize the existing co-culture systems, and design new synthetic co-culture system for large-scale application. OMICS technologies such as genomics, transcriptomics, proteomics, and metabolomics could analyze the biological processes in a high throughput manner. Multi-omics analysis could achieve a "global view" of various members in the microbial co-culture systems, which presents opportunities in understanding synthetic microbial consortia better. This article summarizes recent advances in understanding the mechanisms of synthetic microbial co-culture systems using omics technologies, from the aspects of metabolic network, energy metabolism, signal transduction, membrane transport, stress response, community stability and structural rationality. All these findings could provide important theoretical basis for future application of the microbial co-culture systems with the aids of emerging biotechnologies such as synthetic biology and genome editing.