A Prognostic Risk Signature of Two Autophagy-Related Genes for Predicting Triple-Negative Breast Cancer Outcomes.

Background: Triple-negative breast cancer (TNBC) is recognized as the most aggressive molecular subtype of breast cancer. Recent studies have highlighted the complex role of autophagy in the pathogenesis of TNBC.

Methods: In this study, we evaluated 18,330 genes, including 1111 autophagy-related genes, (ARGs), across 579 TNBC samples from online databases.

Corrigendum: Development of mini-barcode based on chloroplast genome and its application in metabarcoding molecular identification of Chinese medicinal material Radix (Chishao).

[This corrects the article DOI: 10.3389/fpls.2022.

Exploring the biological diversity and source species of medicinal horseflies through metabarcoding.

Horseflies from the Tabanidae family play a significant role in traditional Chinese medicine to treat various health conditions, including coronary heart disease, stroke, headaches, liver cirrhosis, psoriasis, and hepatic carcinoma. There are 27 species of Tabaninae (Tabanidae) used as medicine, and they showed high morphological similarities with those for which medicinal properties have not been reported. Nonetheless, there have been reports suggesting that medicinal crude drugs sometimes contain irrelevant or false species, impacting the drug's efficacy.

The metabarcoding of Grubs: Traditional herbal medicine of Scarabaeidae larvae.

Grubs, called Qicao in China, have a long tradition as herbal medicine in East Asia. These larvae belong to the diverse family Scarabaeidae and are typically harvested from the wild during their immature stage based on morphological characteristics. However, rapid and accurate identification becomes challenging when relying solely on external morphological features, as the lack of clarity on biological sources raises safety concerns for clinical applications.

WITHDRAWN: Chloroplast genome evolution of Berberis (Berberidaceae): Implications for phylogeny and metabarcoding.

After consultation with external experts, the authors acknowledged discrepancies in the classification of certain Berberis samples discussed in the article. Berberis is one of the most complex plant genera, and identifications are very hard, limited to only a handful of experts due to rampant hybridizations and other issues of reticulate evolution. This article has therefore been withdrawn at the request of the authors and with the consent of the editor until the species identification issue has been resolved.

Spatial Distribution and Characterization of the Small-Molecule Metabolites and Hydrolyzed Oligosaccharides in the Rhizome of by Desorption Electrospray Ionization-Mass Spectrometry Imaging and High-Resolution Liquid Chromatography-Mass Spectrometry.

Characterization and spatial distribution studies of the metabolome in plants are crucial for revealing the physiology of plants and developing functional foods. Using the rhizome of as a case, we integrated desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) and high-resolution liquid chromatography/mass spectrometry approaches aimed at characterizing and locating both the small molecules and the macromolecular polysaccharides. Under the optimal conditions, 21 flavonoids and 12 triterpenoids were detected and characterized in different tissues of the rhizome and another 19 components were characterized exclusively by DESI-MSI.

Qualitative identification of lonicerae japonicae flos in traditional chinese medicine using metabarcoding combined with specific mini-barcodes.

Background: Lonicerae japonicae flos, also known as Jinyinhua (JYH), is an important component of traditional Chinese patent medicine (TCPM) products. However, the potential for adulteration and substitution with low-quality materials highlights the need for a reliable and sensitive approach to identify the species composition of TCPM products for consumer safety.

Methods And Results: We used universal ITS2 primers to amplify TCPMs containing JYH.

A novel biological sources consistency evaluation method reveals high level of biodiversity within wild natural medicine: A case study of earthworms as "Guang Dilong".

For wild natural medicine, unanticipated biodiversity as species or varieties with similar morphological characteristics and sympatric distribution may co-exist in a single batch of medical materials, which affects the efficacy and safety of clinical medication. DNA barcoding as an effective species identification tool is limited by its low sample throughput nature. In this study, combining DNA mini-barcode, DNA metabarcoding and species delimitation method, a novel biological sources consistency evaluation strategy was proposed, and high level of interspecific and intraspecific variations were observed and validated among 5376 samples from 19 sampling points regarded as "Guang Dilong" and 25 batches of proprietary Chinese medicines.

Insights into gold-catalyzed formation of aza-heterocycles using benzofuroxans as nitrene transfer reagents: mechanism and origins of chemoselectivity.

Density functional theory (DFT) calculations have been performed to reveal the mechanism of gold(i)-catalyzed annulation of -allylynamides and benzofuroxans as nitrene transfer reagents to construct azaheterocyclic compounds. The calculated results revealed that the reaction mechanism mainly undergoes eight processes. Among the reaction steps, intramolecular nucleophilic attack of the imino N atom on the α-position of activated gold keteniminium is a rate-determining process, which is different from that proposed previously by experiment.

Species diversity analysis of commercial Mantidis Ootheca samples contaminated by store pests based on DNA metabarcoding.

Mantidis Ootheca (Sangpiaoxiao, mantis egg case) is a typical multi-origin Chinese medicinal material. The Chinese Pharmacopoeia stipulates that the Mantidis Ootheca originates from three species of Mantis: Tenodera sinensis, Statilia maculate, and Hierodula patellifera. However, Mantidis Ootheca mainly relies on field collection, which leads to confusion of its actual origin in the market.

Application of Large-Scale Molecular Prediction for Creating the Preferred Precursor Ions List to Enhance the Identification of Ginsenosides from the Flower Buds of .

This work was designed to evaluate the coverage of data-dependent acquisition (DDA) extensively utilized in the untargeted metabolite/component identification in the food sciences and pharmaceutical analysis. Using saponins from the flower buds of (PGF) as an example, precursor ions list (PIL)-including DDA on a Q-Orbitrap mass spectrometer could enable higher coverage than the other four MS acquisition approaches in characterizing PGF ginsenosides. A "Virtual Library of Ginsenoside" containing 13,536 ginsenoside molecules was established by -language-programmed large-scale molecular prediction, which in combination with mass defect filtering could create a new PIL involving 1859 PGF saponin precursors.

Cinobufacini Injection Inhibits the Proliferation of Triple-Negative Breast Cancer Through the Pin1-TAZ Signaling Pathway.

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer (BC), which is characterized by the total absence of human epidermal growth factor receptor 2 (HER2), progesterone receptor (PR), and estrogen receptor (ER) expression. Cinobufacini injection (CI) is the aqueous extract from the dry skin of , which is broadly used for the treatment of malignant tumors. However, the potential mechanism of CI against TNBC has not been fully revealed.

Development of Mini-Barcode Based on Chloroplast Genome and Its Application in Metabarcoding Molecular Identification of Chinese Medicinal Material Radix (Chishao).

Radix (Chishao), a typical multi-origin Chinese medicinal material, originates from the dried roots of or . The previous study suggested that these two commonly used Chishao showed variation in their chemical compositions and clinical efficacies. Therefore, accurate identification of different Chishao species was of great significance for the guide of clinical medication, and timely treatment of patients.

Biological composition analysis of a natural medicine, Faeces Vespertilionis, with complex sources using DNA metabarcoding.

Faeces Vespertilionis is a commonly used fecal traditional Chinese medicine. Traditionally, it is identified relying only on morphological characters. This poses a serious challenge to the composition analysis accuracy of this complex biological mixture.

A strategy for a high enrichment of insect mitochondrial DNA for mitogenomic analysis.

Next-generation sequencing has dramatically fostered insect mitogenomic research in recent years. However, studies on the insect mitochondrial genome (mitogenome) assembly mainly rely on the sequencing data from total DNA, which is not cost-effective as a huge data from nuclear DNA are wasted. Besides, many mitogenomic studies require genomic information from individual organisms, whereas the DNA yield from small individual insects is too low to meet the sequencing requirements.

Tetrandrine promotes angiogenesis via transcriptional regulation of VEGF-A.

Angiogenesis is crucial for tissue damage repair in ischemic cardiovascular diseases. Vascular endothelial growth factor A (VEGF-A) acts as a vital mediator in angiogenesis. In this study, tetrandrine (Tet) was found from 23 herbal chemicals to increase VEGF-A mRNA expression in H9c2 cells and the effect was confirmed in freshly isolated neonatal rat cardiomyocytes.

Insights into molecular structure, genome evolution and phylogenetic implication through mitochondrial genome sequence of Gleditsia sinensis.

Gleditsia sinensis is an endemic species widely distributed in China with high economic and medicinal value. To explore the genomic evolution and phylogenetic relationships of G. sinensis, the complete mitochondrial (mt) genome of G.

Investigation on the stability in plant metabolomics with a special focus on freeze-thaw cycles: LC-MS and NMR analysis to Cassiae Semen (Cassia obtusifolia L.) seeds as a case study.

Metabolomics is a rapid and sensitive tool for the detection of dynamic metabolic compositions in the study of systemic metabolic consequences. However, it is also susceptible to a tiny variation of pre-analytical handling procedures. To provide reproducible results, specific knowledge on metabolites perturbance along with different freeze-thaw cycles (FTCs) is needed for further metabolomics studies.

Leveraging 16S rRNA Microbiome Sequencing Data to Identify Bacterial Signatures for Irritable Bowel Syndrome.

Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder characterized by abdominal pain or discomfort. Previous studies have illustrated that the gut microbiota might play a critical role in IBS, but the conclusions of these studies, based on various methods, were almost impossible to compare, and reproducible microorganism signatures were still in question. To cope with this problem, previously published 16S rRNA gene sequencing data from 439 fecal samples, including 253 IBS samples and 186 control samples, were collected and processed with a uniform bioinformatic pipeline.

The complete mitochondrial genome sequence of (Gerromorpha: Gerridae).

In this study, the complete mitochondrial genome of was sequenced and assembled, which was first reported in . The mitogenome of was 15,391 bp in length, and it contained 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), and a control region (D-loop), the overall base nucleotide compositions encoded was 42.9% A, 14.

The complete mitochondrial genome sequence of (Hemiptera: Gerridae).

In this study, we report the complete mitochondrial genome of . The mitogenome was 15,370 bp in length, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Maximum-likelihood (ML) phylogenetic tree indicated that has a close relationship with .

Transcriptome and Comparative Chloroplast Genome Analysis of : Insights Into Molecular Evolution and Phylogenetic Implication.

(Bunge) Decne is the original plant species of the Chinese herbal medicine Cynanchi Atrati Radix et Rhizoma. The lack of information on the transcriptome and chloroplast genome of hinders its evolutionary and taxonomic studies. Here, the transcriptome and chloroplast genome were assembled and functionally annotated.

The complete chloroplast genome of (Apocynaceae).

() has high medicinal value that belongs to the family Apocynaceae. Here, we reported the complete chloroplast (cp) genome of which was 150,858 bp in length. The cp genome was characterized by a typical quadripartite structure composed of a large single-copy region (LSC 81,919 bp) and a small single-copy region (SSC 17,257 bp) interspersed by a pair of 25,841 bp inverted repeat regions (IRs), and it contained 86 protein-coding genes, eight rRNAs, and 37 tRNAs.