Functional Genomics of Novel Rhabdomyosarcoma Fusion-Oncogenes Using Zebrafish.

Clinical sequencing efforts continue to identify novel putative oncogenes with limited strategies to perform functional validation in vivo and study their role in tumorigenesis. Here, we present a pipeline for fusion-driven rhabdomyosarcoma (RMS) in vivo modeling using transgenic zebrafish systems. This strategy originates with novel fusion-oncogenes identified from patient samples that require functional validation in vertebrate systems, integrating these genes into the zebrafish genome, and then characterizing that they indeed drive rhabdomyosarcoma tumor formation. In this scenario, the human form of the fusion-oncogene is inserted into the zebrafish genome to understand if it is an oncogene, and if so, the underlying mechanisms of tumorigenesis. This approach has been successful in our models of infantile rhabdomyosarcoma and alveolar rhabdomyosarcoma, both driven by respective fusion-oncogenes, VGLL2-NCOA2 and PAX3-FOXO1. Our described zebrafish platform is a rapid method to understand the impact of fusion-oncogene activity, divergent and shared fusion-oncogene biology, and whether any analyzed pathways converge for potential clinically actionable targets.

Delivering Traumatic Brain Injury to Larval Zebrafish.

We describe a straightforward, scalable method for administering traumatic brain injury (TBI) to zebrafish larvae. The pathological outcomes appear generalizable for all TBI types, but perhaps most closely model closed-skull, diffuse lesion (blast injury) neurotrauma. The injury is delivered by dropping a weight onto the plunger of a fluid-filled syringe containing zebrafish larvae. This model is easy to implement, cost-effective, and provides a high-throughput system that induces brain injury in many larvae at once. Unique to vertebrate TBI models, this method can be used to deliver TBI without anesthetic or other metabolic agents. The methods simulate the main aspects of traumatic brain injury in humans, providing a preclinical model to study the consequences of this prevalent injury type and a way to explore early interventions that may ameliorate subsequent neurodegeneration. We also describe a convenient method for executing pressure measurements to calibrate and validate this method. When used in concert with the genetic tools readily available in zebrafish, this model of traumatic brain injury offers opportunities to examine many mechanisms and outcomes induced by traumatic brain injury. For example, genetically encoded fluorescent reporters have been implemented with this system to measure protein misfolding and neural activity via optogenetics.

Methods to Study Liver Disease Using Zebrafish Larvae.

Liver disease affects millions of people worldwide, and the high morbidity and mortality is attributed in part to the paucity of treatment options. In many cases, liver injury self-resolves due to the remarkable regenerative capacity of the liver, but in cases when regeneration cannot compensate for the injury, inflammation and fibrosis occur, creating a setting for the emergence of liver cancer. Whole animal models are crucial for deciphering the basic biological underpinnings of liver biology and pathology and, importantly, for developing and testing new treatments for liver disease before it progresses to a terminal state. The cellular components and functions of the zebrafish liver are highly similar to mammals, and zebrafish develop many diseases that are observed in humans, including toxicant-induced liver injury, fatty liver, fibrosis, and cancer. Therefore, the widespread use of zebrafish larvae for studying the mechanisms of these pathologies and for developing potential treatments necessitates the optimization of experimental approaches to assess liver disease in this model. Here, we describe protocols using staining methods, imaging, and gene expression analysis to assess liver injury, fibrosis, and preneoplastic changes in the liver of larval zebrafish.

Techniques for Developing Reliable Machine Learning Classifiers Applied to Understanding and Predicting Protein:Protein Interaction Hot Spots.

With machine learning now transforming the sciences, successful prediction of biological structure or activity is mainly limited by the extent and quality of data available for training, the astute choice of features for prediction, and thorough assessment of the robustness of prediction on a variety of new cases. In this chapter, we address these issues while developing and sharing protocols to build a robust dataset and rigorously compare several predictive classifiers using the open-source Python machine learning library, scikit-learn. We show how to evaluate whether enough data has been used for training and whether the classifier has been overfit to training data. The most telling experiment is 500-fold repartitioning of the training and test sets, followed by prediction, which gives a good indication of whether a classifier performs consistently well on different datasets. An intuitive method is used to quantify which features are most important for correct prediction.The resulting well-trained classifier, hotspotter, can robustly predict the small subset of amino acid residues on the surface of a protein that are energetically most important for binding a protein partner: the interaction hot spots. Hotspotter has been trained and tested here on a curated dataset assembled from 1046 non-redundant alanine scanning mutation sites with experimentally measured change in binding free energy values from 97 different protein complexes; this dataset is available to download. The accessible surface area of the wild-type residue at a given site and its degree of evolutionary conservation proved the most important features to identify hot spots. A variant classifier was trained and validated for proteins where only the amino acid sequence is available, augmented by secondary structure assignment. This version of hotspotter requiring fewer features is almost as robust as the structure-based classifier. Application to the ACE2 (angiotensin converting enzyme 2) receptor, which mediates COVID-19 virus entry into human cells, identified the critical hot spot triad of ACE2 residues at the center of the small interface with the CoV-2 spike protein. Hotspotter results can be used to guide the strategic design of protein interfaces and ligands and also to identify likely interfacial residues for protein:protein docking.

Accelerating the Discovery and Design of Antimicrobial Peptides with Artificial Intelligence.

Peptides modulate many processes of human physiology targeting ion channels, protein receptors, or enzymes. They represent valuable starting points for the development of new biologics against communicable and non-communicable disorders. However, turning native peptide ligands into druggable materials requires high selectivity and efficacy, predictable metabolism, and good safety profiles. Machine learning models have gradually emerged as cost-effective and time-saving solutions to predict and generate new proteins with optimal properties. In this chapter, we will discuss the evolution and applications of predictive modeling and generative modeling to discover and design safe and effective antimicrobial peptides. We will also present their current limitations and suggest future research directions, applicable to peptide drug design campaigns.

Traditional Chinese Medicine: A promising strategy to regulate the imbalance of bacterial flora, impaired intestinal barrier and immune function attributed to ulcerative colitis through intestinal microecology.

ETHNOPHARMACOLOGICAL RELEVANCE: Globally, plant materials are widely used as an additional and alternative therapy for the treating of diverse diseases. Ulcerative colitis (UC) is a chronic, recurrent and nonspecific inflammation of the bowel, referred to as "modern intractable disease" according to the World Health Organization. With the continuous development of theoretical research in Traditional Chinese Medicine (TCM) and the advantages of TCM in terms of low side effects, TCM has shown great progress in the research of treating UC. AIM OF THIS REVIEW: This review aimed to explore the correlation between intestinal microbiota and UC, summarize research advances in TCM for treating UC, and discuss the mechanism of action of TCM remedies in regulating intestinal microbiota and repairing damaged intestinal barrier, which will provide a theoretical basis for future studies to elucidate the mechanism of TCM remedies based on gut microbiota and provide novel ideas for the clinical treatment of UC. METHODS: We have collected and collated relevant articles from different scientific databases in recent years on the use of TCM in treating UC in relation to intestinal microecology. Based on the available studies, the therapeutic effects of TCM are analysed and the correlation between the pathogenesis of UC and intestinal microecology is explored. RESULTS: TCM is used to further protect the intestinal epithelium and tight junctions, regulate immunity and intestinal flora by regulating intestinal microecology, thereby achieving the effect of treating UC. Additionally, TCM remedies can effectively increase the abundance of beneficial bacteria that produce short-chain fatty acids, decrease the abundance of pathogenic bacteria, restore the balance of intestinal microbiota, and indirectly alleviate intestinal mucosal immune barrier dysfunction and promote the repair of damaged colorectal mucosa. CONCLUSION: Intestinal microbiota is closely related to UC pathogenesis. The alleviation of intestinal dysbiosis can be a potential novel therapeutic strategy for UC. TCM remedies can exert protective and therapeutic effects on UC through various mechanisms. Although intestinal microbiota can aid in the identification of different TCM syndromes types, further studies are needed using modern medical technology. This will improve the clinical therapeutic efficacy of TCM remedies in UC and promote the application of precision medicine.

Cannabis sativa L. roots from Northeast Brazil reduce abdominal contortions in a mouse model of primary dysmenorrhea.

ETHNOPHARMACOLOGICAL RELEVANCE: Although the root of Cannabis sativa L. has been mentioned in some regions, such as the Vale do São Francisco, for its potential traditional medicinal use as an anti-inflammatory, anti-asthmatic, and against gastrointestinal diseases, it has received little exploration and discussion. AIM OF THE STUDY: This study aimed to perform a chemical analysis of an aqueous extract of Cannabis sativa roots (AqECsR) and evaluate its pharmacological effects against uterine disorders, in vivo and ex vivo, in rodents. MATERIALS AND METHODS: The roots were provided by the Brazilian Federal Police, and the freeze-dried extract was used for the chemical analysis of the AqECsR by high performance liquid chromatography coupled with mass spectrometry (HPLC-MS). The sample was subsequently used in three doses for pharmacological assays (12.5, 25, and 50 mg/kg), which included the spasmolytic activity test and the primary dysmenorrhea test. The primary dysmenorrhea test aimed to verify the effect of AqECsR on induced abdominal contortions in female mice in vivo and to perform a morphometric analysis of the organs. Association tests at subtherapeutic doses of AqECsR with antidysmenorrheic drugs were also performed. RESULTS: The data obtained by HPLC-MS suggested the presence of four substances: cannabisativine, anhydrocannabisativine, feruloyltyramine, and p-coumaroyltyramine. In the pharmacological assays, the AqECsR showed no spasmolytic effect. However, in the antidysmenorrheal activity test, AqECsR demonstrated a significant in vivo effect of reducing oxytocin-induced abdominal contortions. Morphometric analysis of the uterus showed no significant organ enlargement effect, and the association of AqECsR with subtherapeutic doses of three drugs used in antidysmenorrheal therapy (mefenamic acid, scopolamine, and nifedipine) showed an effect in reducing abdominal contortions. CONCLUSIONS: In conclusion, AqECsR contains four chemical compounds and exhibits an antidysmenorrheic effect both alone and in association with drugs, reducing abdominal contortions in female mice without generating organ enlargement in the animals. Further studies are needed to prove the mechanism of action by which AqECsR promotes its effect on primary dysmenorrhea and to explore its associations.

Bushen Antai recipe ameliorates immune microenvironment and maternal-fetal vascularization in STAT3-deficient abortion-prone mice.

ETHNOPHARMACOLOGICAL RELEVANCE: Spontaneous abortion (SA) is an intricate disorder affecting women of reproductive age. Previous studies have confirmed the indispensable role of signal transducer and activator of transcription (STAT) 3 in normal pregnancy. Bushen Antai recipe (BAR) is a satisfactory formula commonly used in practice, based on the rationale of traditional Chinese medicine (TCM) for SA. AIM OF THE STUDY: The current study explores the potential therapeutic effects and mechanistic insights of BAR in STAT3-deficient abortion-prone mice. MATERIALS AND METHODS: A STAT3-deficient abortion-prone mouse model was developed using intraperitoneal injection of stattic from embryo day (ED) 5.5 to ED9.5 among pregnant females (C57BL/6). We separately administered BAR1 (5.7 g/kg), BAR2 (11.4 g/kg), progesterone (P4), or distilled water at 10 ml/kg/day from ED0.5 until ED10.5. The embryo resorption rate and placenta-uterus structure were observed on ED10.5. The systemic immune status was examined by analyzing the frequency of immunosuppressive myeloid-derived suppressor cells (MDSCs), the ratio of two macrophage (M) subtypes, and the protein expression of associated molecules. Morphological observation, immunohistochemistry, and western blotting were used to evaluate the vascularization conditions at the maternal-fetal interface. RESULTS: BAR1, BAR2, or P4 treatment exerted remarkable effects in alleviating embryo resorption rate and disordered placental-uterus structure in STAT3-deficient abortion-prone mice. Western blotting indicated the deficiency of phosphorylated STAT3 and two prime target molecules, PR and HIF-1α, at the maternal-fetal interface under STAT3 inhibition. Simultaneously, BAR2 treatment significantly upregulated their expression levels. The systemic immune environment was disrupted, indicated by the reduced serum cytokine concentrations, MDSCs frequency, M2/M1 ratio, and the expression of immunomodulatory factors. Nonetheless, BAR2 or P4 treatment revived the immune tolerance for semi-allogenic embryos by enhancing the immune cells and factors. Besides, the western blot and immunohistochemistry results revealed that BAR2 or P4 treatment upregulated VEGFA/FGF2 and activated ERK/AKT phosphorylation. Therefore, BAR2 or P4 facilitated vascularization at the maternal-fetal interface in STAT3-deficient abortion-prone mice. CONCLUSIONS: BAR sustained pregnancy by reviving the systemic immune environment and promoting angiogenesis at the maternal-fetal interface in STAT3-deficient abortion-prone mice.

Beneficial biological effects of Flavokawain A, a chalcone constituent from kava, on surgically induced endometriosis rat model.

ETHNOPHARMACOLOGICAL RELEVANCE: Shrub kava has long been grown and utilized, primarily in the South Pacific region, for ceremonial, religious, and social occasions. It has been used as a pain reliever and muscle relaxant in medicinal practices from the eighteenth century. Interestingly, relatively low incidence of lung cancer may attribute to the high consumption of kava products in this region. AIM OF THE STUDY: Kava extracts were used to produce the kava chalcones Flavokawain A, B and C, which have a variety of bioactivities. In the present study, we show that Flavokawain A has positive effects on endometriosis. MATERIALS AND METHODS: The endometriosis rat model was surgically induced by the autologous transplantation of endometrial tissue. Rats were evaluated for clinical ratings and lesion volume following a 6-week Flavokawain A therapy. Peritoneal fluid and blood samples were taken and ELISA assay was used to measure the cytokines and chemokines levels. Transcriptional and expression levels of Akt, PI3K, NF-kB, iNOS, Bcl-2, Bax and caspase-3 were evaluated by Western blotting and RT-qPCR. Implanted tissue sections of the rats were also analyzed by immunofluorescent and histopathological staining. RESULTS: Lesion volumes and adhesion scores were successfully decreased. Blood and peritoneal fluid levels of associated cytokines and chemokines were markedly down-regulated. Besides, Flavokawain A also mediated cell apoptosis of endometrial implants. Additionally, VEGF expression was reduced, which inhibited the angiogenesis process. As for the expression of Akt, p-Akt, PI3K, p-PI3K, and NF-kB in endometriosis lesions, Flavokawain A significantly reduced them. CONCLUSION: Flavokawain A has beneficial effects on the surgically induced endometriosis rat model, by reducing inflammation, promoting apoptosis, and decreasing angiogenesis. Our findings suggest that these effects may be mediated through the regulation of PI3K/Akt and NF-κB signaling pathways.

The traditional use of native Brazilian plants for male sexual dysfunction: Evidence from ethnomedicinal applications, animal models, and possible mechanisms of action.

ETHNOPHARMACOLOGICAL RELEVANCE: Sexual dysfunction is a multifactorial health condition characterized by distressing disturbances in the sexual response and libido, leading to an inability to maintain penile erection and achieve pleasure. Considering the huge Brazilian biodiversity, many plants are traditionally used for aphrodisiac purposes. However, the use of native medicinal plants as sexual boosters in Brazil has been poorly studied. AIM OF THE STUDY: This review focuses on the composition, pharmacology, and results of experimental trials of the main native plants used in Brazilian folk medicine with alleged aphrodisiac effects. We aimed to provide a state-of-the-art reference for research on herbs for the treatment of male sexual dysfunction by summarizing and discussing the main studies found. MATERIALS AND METHODS: The relevant information was collected by searching keywords (aphrodisiac, sexual tonic, sexual stimulant, sexual vigor stimulant, sexual impotency, erectile dysfunction, etc.) from books containing primary surveys conducted in the original communities and bibliographic surveys prepared by authors linked to the national academic and scientific environment edited in Brazil. Preclinical and clinical studies of the compiled plant species were performed using scientific databases (Scopus, PubMed, SciELO, and SciFinder). RESULTS: Seventy-four plant species belonging to 44 families used in Brazil to treat sexual dysfunction were compiled from ethnopharmacological literature. Fourteen plants, including Pfaffia glomerata (Spreng.) Pedersen, Aspidosperma quebracho-blanco Schltdl., Anemopaegma arvense (Vell.) Stellfeld ex de Souza, Mimosa pudica L., Heteropterys tomentosa A. Juss., Trichilia catigua A. Juss., and Turnera diffusa Willd. ex Schult. were pharmacologically studied to confirm these therapeutic properties. Probable modes of action include antioxidant and androgenic activities, inhibition of the PDE5 enzyme, increase in NO levels, and activation of dopaminergic and noradrenergic pathways. In addition, several different species popularly known as "catuaba" were identified, leading to adulterations and controversial effects. CONCLUSION: The overall results of the present review of Brazilian folk literature reveal that Brazil has a long tradition of using plants with potential aphrodisiac effects. However, further research is required to identify, characterize, and standardize the active ingredients and herbal preparations used in aphrodisiacs.

Antrodia salmonea suppresses epithelial-mesenchymal transition/metastasis and Warburg effects by inhibiting Twist and HIF-1α expression in Twist-overexpressing head and neck squamous cell carcinoma cells.

ETHNOPHARMACOLOGICAL RELEVANCE: Antrodia salmonea (AS), linked to the genus Taiwanofungus, is a medicinal fungus, and exhibits anti-inflammatory, anti-oxidant, and tumor inhibiting properties. AIM OF THE STUDY: In this study, we investigated the metabolic reprogramming and anti-metastasis/epithelial-mesenchymal transition (EMT) effects of AS exposure in Twist-overexpressing head and neck squamous cell carcinoma (HNSCC, OECM-1 and FaDu-Twist) cells. MATERIALS AND METHODS: MTT assay, Western blot, migration/invasion assay, immunofluorescence, glucose uptake assay, lactate assay, oxygen consumption rate (OCR)/Extracellular acidification rate (ECAR) assay, Liquid Chromatography-Electrospray Ionization Tandem Mass Spectrometry (LC-ESI-MS), and qRT-PCR experimental techniques were used to evaluate the therapeutic potential of AS treatment in HNSCC cells. RESULTS: This study showed that AS exhibits anti-EMT and anti-metastatic effects as well as metabolic reprogramming in Twist-overexpressing HNSCC cells. AS exposure inhibited Twist and hypoxia-inducible factor-1α (HIF-1α) protein and/or mRNA expression in Twist-overexpressing OECM-1 and FaDu-Twist cells. AS markedly suppressed EMT by enhancing the expression of E-cadherin; while the N-cadherin was suppressed. Furthermore, glucose uptake and lactate accumulation, together with HIF-1α-regulated glycolysis genes were diminished by AS in OECM-1 cells. AS decreased the ECAR, and enhanced the OCR together with basal respiration, ATP production, maximal respiration, and spare respiratory capacity under normoxia and hypoxia (CoCl2) in OECM-1 cells. There was a marked reduction in the level of glycolytic intermediate's; while TCA cycle metabolites were increased by AS treatment in OECM-1 cells. CONCLUSIONS: We concluded that AS treatment suppresses EMT/metastasis and Warburg effects through Twist and HIF-1α inhibition in Twist-overexpressing HNSCC cells.

Tumor-associated macrophage-derived exosomal miR-513b-5p is a target of jianpi yangzheng decoction for inhibiting gastric cancer.

ETHNOPHARMACOLOGICAL RELEVANCE: Jianpi Yangzheng decoction (JPYZ) possesses a potential anti-tumor activity in gastric cancer. However, potential effect of JPYZ on regulating tumor-associated macrophage (TAM)-derived exosomes to affect gastric cancer is still unclear. AIM OF STUDY: We aimed to clarify the role of tumor-associated macrophage derived exosomes (TAM-exos) in invasive and metastasis of gastric cancer and the mechanism of JPYZ regulate TAM-exos against gastric cancer. MATERIALS AND METHODS: Flow cytometry was performed to demonstrate whether JPYZ involved in TAM polarization. After JPYZ treatment, TAM conditioned medium (TAM-CM)/TAM-exos were co-cultured with gastric cancer cells and were detected by wound healing and transwell assay. Transcriptome sequencing and bioinformatics analysis predicted the exosomal miRNA after JPYZ intervention in TAM. miRNA mimic and inhibitor were used to verify the effect of miRNA in exosomes on gastric cancer cells. Q-PCR and luciferase reporter assay were employed to clarify the targeting relationship between miRNA and target gene. Western blot assay detected the expression levels of epithelial-mesenchymal transition (EMT) markers and related signaling pathways proteins. RESULTS: We firstly demonstrated that TAM-CM intervened by JPYZ significantly inhibited the invasion and migration of gastric cancer. Furthermore, exosomes in TAM supernatants play a key role in migration of gastric cancer. Meanwhile, transcriptome sequencing and q-PCR revealed that miR-513b-5p expression was significantly reduced in TAM-exos intervened by JPYZ. And miR-513b-5p in TAM aggravated TAM-exos mediated invasion and migration of gastric cancer cells, the inhibitor of miR-513b-5p reversed TAM-exos mediated promotion. Bioinformatics analysis and luciferase reporter assay confirmed that PTEN was a direct target of miR-513b-5p in gastric cancer. MiR-513b-5p inhibited PTEN to activate AKT/mTOR signaling pathway thus promoting gastric cancer invasion and metastasis in vivo and in vitro. Importantly, JPYZ inhibited TAM derived exosomal miR-513b-5p, and alleviated AKT/mTOR activation by PTEN depended manner in gastric cancer. CONCLUSION: TAM-exos containing miR-513b-5p lead to gastric cancer invasion and migration. Our findings clarify a novel TAM-exos mechanism of JPYZ for inhibiting gastric cancer progression.

Chlorophytum borivilianum aqueous root extract prevents deterioration of testicular function in mice and preserves human sperm function in hydrogen peroxide (H2O2)-induced oxidative stress.

ETHNOPHARMACOLOGICAL RELEVANCE: Chlorophytum borivilianum (C. borivilianum) (CB) has traditionally been used to treat male sexual dysfunctions and has been claimed to possess aphrodisiac properties. AIM OF THE STUDY: To investigate the ability of CB to ameliorate H2O2-induced oxidative stress in testes and sperm in mice and prevent H2O2-induced oxidative in human sperm. MATERIALS AND METHODS: Oxidative stress was induced in male mice by pre-exposure to 2% H2O2 orally for seven consecutive days, followed by 100 and 200 mg/kg b. w. administration. CB for another seven days. At the end of treatment, mice were sacrificed and testes and epididymal sperm were harvested. Serum FSH, LH and testosterone levels were measured and sperm parameters were obtained. Meanwhile, oxidative stress levels in mice testes and sperm, steroidogenesis and spermatogenesis markers in mice testes were assessed by molecular biological techniques. In another experiment, sperm from thirty-two healthy fertile men were incubated with 200 µM H2O2 and CB (100 and 200 µg/ml) simultaneously and were then evaluated for sperm parameter changes. RESULTS: In mice, CB administration ameliorates persistent increases in oxidative stress and decreases in anti-oxidative enzyme levels in testes and sperm following H2O2 pre-exposure. Additionally, CB also helps to ameliorate deterioration in sperm parameters and testicular steroidogenesis and spermatogenesis and restores the serum FSH, LH and testosterone levels near normal in mice. In humans, CB helps to prevent deterioration in sperm parameters following H2O2 exposure. CONCLUSION: CB is potentially useful to preserve the male reproductive capability and subsequently male fertility in high oxidative stress conditions.

Adjuvant role of Salvia miltiorrhiza bunge in cancer chemotherapy: A review of its bioactive components, health-promotion effect and mechanisms.

ETHNOPHARMACOLOGICAL RELEVANCE: Chemotherapy is a common cancer treatment strategy. However, its effectiveness is constrained by toxicity and adverse effects. The Lamiaceae herb Salvia miltiorrhiza Bunge has a long history of therapeutic use in the treatment of blood stasis illnesses, which are believed by traditional Chinese medicine to be connected to cancer. AIM OF THE STUDY: This review summarized the common toxicity of chemotherapy and the potential chemo-adjuvant effect and mechanisms of active ingredients from S. miltiorrhiza, hoping to provide valuable information for the development and application of S. miltiorrhiza resources. MATERIALS AND METHODS: The literatures were retrieved from PubMed, Web of Science, Baidu Scholar and Google Scholar databases from 2002 to 2022. The inclusion criteria were studies reporting that S. miltiorrhiza or its constituents enhanced the efficiency of chemotherapy drugs or reduced the side effects. RESULTS: Salvianolic acid A, salvianolic acid B, salvianolic acid C, rosmarinic acid, tanshinone I, tanshinone IIA, cryptotanshinone, dihydrotanshinone I and miltirone are the primary adjuvant chemotherapy components of S. miltiorrhiza. The mechanisms mainly involve inhibiting proliferation, metastasis, and angiogenesis, inducing apoptosis, regulating autophagy and tumor microenvironment. In addition, they also improve chemotherapy drug-induced side effects. CONCLUSIONS: The bioactive compounds of S. miltiorrhiza are shown to inhibit proliferation, metastasis, and angiogenesis, induce apoptosis and autophagy, regulate immunity and tumor microenvironment when combined with chemotherapy drugs. However, further clinical studies are required to validate the current studies.

In vitro anti-bactrical activity and its preliminary mechanism of action of the non-medicinal parts of Sanguisorba officinalis L. against Helicobacter pylori infection.

ETHNOPHARMACOLOGICAL RELEVANCE: Sanguisorba officinalis L. (S. officinalis L.), known as Di Yu (DY) in Traditional Chinese Medicine (TCM), are used to treat burns, vomiting of blood, asthma, intestinal infections, and dermatitis. It has been reported that the root of DY has a significant inhibitory effect on Helicobacter pylori (H. pylori). However, there is currently little research on the composition analysis and anti-H. pylori infection properties of the non-medicinal parts of DY, such as its stems, leaves, and flowers. AIM OF STUDY: The commonly used eradication therapies for H. pylori infection are antibiotic-based therapies. With the increasing antibiotic resistance of H. pylori, it is urgent to find effective alternative therapies. To find alternative therapies and increase the utilization of DY, this study aims to investigate the phytochemistry profile, in vitro anti-H. pylori activity, and preliminary antibacterial mechanism of the non-medicinal parts of DY. MATERIALS AND METHODS: The non-medicinal parts of DY extracts were obtained by using hot water reflux method. The chemical composition of these extracts was analyzed using colorimetric method, high-performance liquid chromatography (HPLC), and ultra-high-performance liquid chromatography-electrospray ionization-mass spectrometry (UPLC-ESI-MS). The in vitro anti-H. pylori activity was investigated using broth microdilution method, checkerboard dilution method, time-kill curve, time-inhibition curve, scanning electron microscopy, and transmission electron microscopy. Transcriptional sequencing technology was used to study the effect of DY stems and flowers on the gene expression of H. pylori and explore possible antibacterial mechanisms. RESULTS: The non-medicinal parts of DY contain abundant phytochemicals, such as total phenols and total flavonoids, and possess strong inhibitory and bactericidal activity against both standard and clinical strains of H. pylori in vitro. The MIC was 80-1280 µg/mL and the MBC was 80-2560 µg/mL, and the strength of the antibacterial effects was dependent on the concentration of phytochemicals (total polyphenols, gallic acid and ellagic acid). In addition, the combination of non-medicinal parts of DY with antibiotics, such as amoxicillin, metronidazole, levofloxacin, and clarithromycin, did not result in any antagonistic effects. All of them could disrupt the morphology, internal microscopic and cell wall structures of H. pylori thereby acting as an inhibitor. The mechanism of action was found to be the disruption of H. pylori morphology, internal microstructure, and cell wall. Transcriptomic analysis showed that the non-medicinal parts of DY significantly regulated the gene expression of H. pylori, especially the metabolic pathway. CONCLUSIONS: This study analyzed the chemical composition of the non-medicinal parts of DY and confirmed its inhibitory and bactericidal activities against H. pylori, both standard and clinical strains. Additional, the mechanism of inhibition involves disrupting the structure of H. pylori cells, altering gene expression, and interfering with bacterial metabolic pathways. This study provides a reference for further resource utilization and the development of H. pylori drugs using the non-medicinal parts of DY.

Licochalcone A promotes renewal of intestinal mucosa through modulating uc.173.

ETHNOPHARMACOLOGICAL RELEVANCE: Licorice can nourish Pi (spleen) and thereby strengthening the digestive system according to the theory of traditional Chinese medicine. Licorice has been generally used in the compound prescription to treat intestinal inflammatory disease. Licochalcone A (Lico A) is one of the characteristic molecules from licorice. T-UCRs, which are transcribed from ultraconserved regions, are a new class of long noncoding RNAs related to the renewal of intestinal epithelial renewal. AIM OF THE STUDY: This study aimed to investigate the effect and the uc.173-related mechanism of Lico A on intestinal epithelial renewal. MATERIALS AND METHODS: IE-6 and Caco-2 cells were used to evaluate the effect of Lico A on apoptosis, proliferation, and migration of IECs. The intestinal organoid was used to investigate ex vivo effect and mechanism of Lico A promoting intestinal organoid development. C57BL/6J mice (both normal and uc.173-deficient ones) were used to examine the in vivo effect of Lico A on the renewal of intestinal mucosa. RESULTS: The expression of three T-UCRs related to the intestinal mucosa renewal was altered in Lico A-treated IECs. Lico A promoted the proliferation and inhibited the apoptosis of IECs through uc.173/miR-195 pathway. The development of intestinal organoids and the renewal of intestinal mucosa of mice subjected to the 48-h FAST were all promoted by the treatment of Lico A. Moreover, the growth arrest of uc.173-deficient intestinal organoids and the atrophy of intestinal mucosa in uc.173-deficient mice could be rescued by the Lico A administration. CONCLUSION: Results in this paper suggest that targeting T-UCRs may be the novel therapeutic approach for the promotion of epithelial regeneration, and through stimulating the regeneration of intestinal mucosa, Lico A may become a new therapeutic agent for the maintenance of intestinal epithelial integrity.

One master and two servants: One Zr(â £) with two ligands of TCPP and NH2-BDC form the MOF as the electrochemiluminescence emitter for the biosensing application.

Here we put forward an innovative "one master and two servants" strategy for enhancing the ECL performance. A novel ECL luminophore named Zr-TCPP/NH2-BDC (TCPP@UiO-66-NH2) was synthesized by self-assembly of meso-tetra(4-carboxyphenyl)porphine (TCPP) and 4-aminobenzoic acid (NH2-BDC) with Zr clusters. TCPP@UiO-66-NH2 has a porous structure and a highly ordered structure, which allows the molecular motion of TCPP to be effectively confined, thereby inhibiting nonradiative energy transfer. Importantly, TCPP@UiO-66-NH2 has a higher and more stable ECL signal. To further improve the sensitivity of the sensor, we use polydopamine-coated manganese dioxide (PDA@MnO2), which has a double quenching effect, as the quencher. The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2-N) is one of the ideal markers for the early diagnosis of COVID-19, and its sensitivity detection is of great significance for the prevention and treatment of COVID-19. Thus, we constructed a quenching-type ECL sensor for the ultrasensitive detection of the SARS-CoV-2-N. Its linear range is 10 fg/mL∼1 µg/mL and the calculated detection limit is 1.4 fg/mL (S/N = 3). The spiked recoveries are 97.40-103.8%, with the relative standard deviations (RSD) under 3.0%. More importantly, the technique offers a viable way to identify and diagnose viral infections early.

Revolutionizing SARS-CoV-2 omicron variant detection: Towards faster and more reliable methods.

The emergence of the highly contagious Omicron variant of SARS-CoV-2 has inflicted significant damage during the ongoing COVID-19 pandemic. This new variant's significant sequence changes and mutations in both proteins and RNA have rendered many existing rapid detection methods ineffective in identifying it accurately. As the world races to control the spread of the virus, researchers are urgently exploring new diagnostic strategies to specifically detect Omicron variants with high accuracy and sensitivity. In response to this challenge, we have compiled a comprehensive overview of the latest reported rapid detection techniques. These techniques include strategies for the simultaneous detection of multiple SARS-CoV-2 variants and methods for selectively distinguishing Omicron variants. By categorizing these diagnostic techniques based on their targets, which encompass protein antigens and nucleic acids, we aim to offer a comprehensive understanding of the utilization of various recognition elements in identifying these targets. We also highlight the advantages and limitations of each approach. Our work is crucial in providing a more nuanced understanding of the challenges and opportunities in detecting Omicron variants and emerging variants.

Highly sensitive enantioselective spectrofluorimetric determination of R-/S-mandelic acid using l-tryptophan-modified amino-functional silica-coated N-doped carbon dots as novel high-throughput chiral nanoprobes.

Amino-functional silica-coated N-doped carbon dots (NH2-SiO2-CDs) were covalently modified by l-tryptophan (chiral selector) by producing an amide bond between carboxyl groups of L-try and amino groups of NH2-SiO2-CDs to develop a novel high throughput chiral nanoprobes (L-try-CONH-SiO2-CDs) for highly sensitive and enantioselective quantification of S-/R-mandelic acid (S-/R-Man). The method showed a great difference between S- and R-isomers (enantioselectivity coefficient = 4.17) due to the ultra-stability of the Meisenheimer complex that was formed between S-isomer and nanoprobe (KS-Man/KR-man = 2122.7, where K is the binding-constant). At optimal experimental conditions, two linear ranges of 0.5-25.0 (LOD of 0.05 µM) and 0.5-22.0 µM (LOD of 0.27 µM) for S- and R-Man, respectively, along with an enhanced sensitivity toward S-isomer (about 5.7-fold higher than R-isomer) were attained. High selectivity for the determination of mandelic acid was achieved compared to metal ions, amino acids, and sugars that commonly coexist with it. Intra-day as well as inter-day assays, respectively, showed RSD values of about 3.2 and 3.9%. The mechanistic studies were performed for proving the enantioselective behavior of the developed nanoprobe. The method was then used for S-/R-mandelic acid determination in bio-samples. The figures of merit for the method were found to be better than those already reported for enantioselective detection of R-/S-Man.

Normalization methods in mass spectrometry-based analytical proteomics: A case study based on renal cell carcinoma datasets.

Normalization is a crucial step in proteomics data analysis as it enables data adjustment and enhances comparability between datasets by minimizing multiple sources of variability, such as sampling, sample handling, storage, treatment, and mass spectrometry measurements. In this study, we investigated different normalization methods, including Z-score normalization, median divide normalization, and quantile normalization, to evaluate their performance using a case study based on renal cell carcinoma datasets. Our results demonstrate that when comparing datasets by pairs, both the Z-score and quantile normalization methods consistently provide better results in terms of the number of proteins identified and quantified as well as in identifying statistically significant up or down-regulated proteins. However, when three or more datasets are compared at the same time the differences are found to be negligible.