The complete chloroplast genome of Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen. 1834 (Lamiaceae) and its phylogenetic analysis.

Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen is a perennial herb with much-branched stems native to Nei Mongol, Ningxia, Gansu, N Shaanxi. It can be used clinically as a hemostatic agent. The chloroplast genome length is 151,466 bp. It contained two inverted repeat regions of 25,660 bp each, a large single-copy region of length 82,504 bp, and a small single-copy region of length 17,642 bp. Also, the GC content is 38.6%. There were 133 genes annotated, including 88 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic tree was constructed using Bayesian method for plastome data of 29 species. The entire chloroplast genome of L. ilicifolius within the Lamiaceae is the first to reveal genetic taxonomy at the molecular level, and the new phylogenetic tree data can be used for future evolutionary studies.

The complete chloroplast genome of Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (Malvaceae).

Grewia biloba var. parviflora (Bunge) Hand.-Mazz. (1933), a shrub or small tree, is native to northern and southern China. It is an excellent relief and medicinal plant. The complete chloroplast genome is 158,043 bp in length, with a large single-copy region of 86,957 bp, a small single-copy region of 20,138 bp, two inverted repeat regions of 25,474 bp each, and a GC content of 37.4%. There were 129 genes annotated, including 84 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic trees are constructed using plastome data from 38 species and the maximum-likelihood method. The results of the chloroplast genome-wide analysis and the phylogenetic tree show the taxonomic phylogeny of the G. biloba var. parviflora in relation to other species, increasing the accuracy of the phylogenetic classification of the plant.

The role of the ERK signaling pathway in promoting angiogenesis for treating ischemic diseases.

The main treatment strategy for ischemic diseases caused by conditions such as poor blood vessel formation or abnormal blood vessels involves repairing vascular damage and encouraging angiogenesis. One of the mitogen-activated protein kinase (MAPK) signaling pathways, the extracellular signal-regulated kinase (ERK) pathway, is followed by a tertiary enzymatic cascade of MAPKs that promotes angiogenesis, cell growth, and proliferation through a phosphorylation response. The mechanism by which ERK alleviates the ischemic state is not fully understood. Significant evidence suggests that the ERK signaling pathway plays a critical role in the occurrence and development of ischemic diseases. This review briefly describes the mechanisms underlying ERK-mediated angiogenesis in the treatment of ischemic diseases. Studies have shown that many drugs treat ischemic diseases by regulating the ERK signaling pathway to promote angiogenesis. The prospect of regulating the ERK signaling pathway in ischemic disorders is promising, and the development of drugs that specifically act on the ERK pathway may be a key target for promoting angiogenesis in the treatment of ischemic diseases.

The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis.

The plant-associated microbiome has an effect on plant growth. Pulsatilla chinensis (Bge.) Regel is an important Chinese medicinal plant. Currently, there is little understanding of the P. chinensis-associated microbiome and its diversity and composition. Here, the core microbiome associated with the root, leaf, and rhizospheric soil compartments of P. chinensis from five geographical locations was analyzed by the metagenomics approach. The alpha and beta diversity analysis showed that the microbiome associated with P. chinensis was shaped by the compartment, especially in the bacterial community. The geographical location had little influence on microbial community diversity associated with root and leaf. Hierarchical clustering distinguished the microbial communities of rhizospheric soil based on their geographical location and among the soil properties, pH was showed the more stronger effect on the diversity of rhizospheric soil microbial communities. Proteobacteria was the most dominant bacterial phylum in the root, leaf, and rhizospheric soil. Ascomycota and Basidiomycota were the most dominant fungal phyla in different compartments. Rhizobacter, Anoxybacillus, and IMCC26256 were the most important marker bacterial species for root, leaf, and rhizospheric soil screened by random forest, respectively. The fungal marker species for root, leaf, and rhizospheric soil were not only different across the compartments but also the geographical locations. Functional analysis showed that P. chinensis-associated microbiome had the similar function which had no obvious relationship with geographical location and compartment. The associated microbiome indicated in this study can be used for identifying microorganisms related to the quality and growth of P. chinensis. KEY POINTS: • Microbiome associated with P. chinensis was shaped by the compartment • Microbiome composition and abundance associated with rhizospheric soil were affected by the geographical location • Compared with fungi, bacterial associated with P. chinensis composition and diversity were more stable in different geographical locations and compartments.

The complete chloroplast genome sequence of Syringa oblata Lindl. var. alba Hort. ex Rehd. 1763 (Oleaceae).

Syringa oblata var. alba is a shrub or a small tree from China with high ornamental, medicinal, and edible value. Here, we present its first complete chloroplast genome. The entire circular genome is 155,648 bp in length, with large single-copy (LSC) length of 86,247, small single-copy (SSC) length of 17,937, inverted repeat (IR) length of 25,732, and GC content of 37.9%. One hundred and thirty-two genes, including 88 protein-coding, 36 tRNA, and eight rRNA genes were predicted. A phylogenetic tree of 25 plant species was constructed based on the maximum-likelihood method, indicating that S. oblata var. alba, S. vulgaris, and S. oblata form a sister group. This study will provide valuable basic information for phylogeny, species identification, and varieties breeding of this species.

Continuous Spatiotemporal Therapy of A Full-API Nanodrug via Multi-Step Tandem Endogenous Biosynthesis.

Nanomedicine holds great promise to enhance cancer therapy. However, low active pharmaceutical ingredient (API) loading content, unpredictable drug release, and potential toxicity from excipients limit their translational capability. We herein report a full-API nanodrug composed of FDA-approved 5-aminolevulinic acid (ALA), human essential element Fe3+, and natural bioactive compound curcumin with an ideal API content and pH-responsive release profile for continuous spatiotemporal cancer therapy achieved by multi-step tandem endogenous biosynthesis. First, ALA enzymatically converts into photosensitizer protoporphyrin IX (PpIX). Afterward, multiple downstream products including carbon monoxide (CO), Fe2+, biliverdin (BV), and bilirubin (BR) are individually biosynthesized through the PpIX-heme-CO/Fe2+/BV-BR metabolic pathway, further cooperating with released Fe3+ and curcumin, ultimately eliciting mitochondria damage, membrane disruption, and intracytoplasmic injury. This work not only provides a paradigm for exploiting diversified metabolites for tumor suppression, but also presents a safe and efficient full-API nanodrug, facilitating the practical translation of nanodrugs.

Advanced Nanomedicine: Redefining Therapeutic Paradigms for Inflammatory Bowel Disease.

Inflammatory bowel disease (IBD), a chronic and recurrent gastrointestinal inflammatory disorder with a variety of painful clinical manifestations and an increased risk of cancerization or death, has become an emerging challenge to global healthcare due to its rapidly increasing incidence. At present, there is no efficient cure against IBD because of the elusive etiology and pathogenesis of IBD. Therefore, the development of alternative therapeutic strategies with positive clinical efficacy and reduced side effects is urgently needed. In recent years, the great prosperity of nanomedicine promoted by a variety of advanced nanomaterials is redefining more attractive and promising therapeutic strategies for IBD owing to their advantages in the physiological stability, bioavailability, and targeting of inflammatory sites. In this review, firstly the basic characteristics of healthy and inflammatory intestinal microenvironments are presented. Then, different administration routes and targeting strategies of nanotherapeutics for IBD treatment are reviewed. Subsequently, a specific focus is placed on the introduction of nanotherapeutic treatments based on different IBD pathogenesis. Finally, some future challenges and perspectives of the currently developed nanomedicines for IBD treatment are provided. It is believed that the above topics will attract researchers from various fields including medicine, biological sciences, materials, chemistry and pharmaceutics.

RRP Regulates Autophagy through the AMPK Pathway to Alleviate the Effect of Cell Senescence on Atherosclerosis.

Autophagy is closely associated with atherosclerosis and other cardiovascular diseases (CVD). Compound Danshen prescription is widely used as a clinical antiatherosclerotic drug. In our previous studies, we have shown that the combined active component, ginsenoside Rg1-notoginsenoside R1-protocatechualdehyde (RRP), can effectively alleviate endothelial dysfunction and reduce atherosclerotic plaques. However, the association between cellular senescence, caused by reduced autophagy, and atherosclerosis remains unclear. In this study, we investigated whether RRP can enhance autophagy and alleviate cell senescence through the AMPK pathway. Our results showed that RRP reduced the secretion of inflammatory factors in the serum of atherosclerotic mice, enhanced autophagy, and alleviated aortic aging in mice, thus reducing atherosclerotic plaques. In human aortic endothelial cells (HAECs), RRP effectively enhanced autophagy and inhibited senescence by activating the AMPK pathway. When AMPKα was silenced, the effect of RRP was inhibited, thus reversing its antiaging effect. Overall, our results show that RRP regulates autophagy through the AMPK pathway, thereby inhibiting cell senescence and alleviating the progression of atherosclerosis, suggesting that RRP may be a potential candidate drug for the treatment of atherosclerosis.

The burdock database: a multi-omic database for Arctium lappa, a food and medicinal plant.

BACKGROUND: Burdock is a biennial herb of Asteraceae found in Northern Europe, Eurasia, Siberia, and China. Its mature dry fruits, called Niu Bang Zi, are recorded in various traditional Chinese medicine books. With the development of sequencing technology, the mitochondrial, chloroplast, and nuclear genomes, transcriptome, and sequence-related amplified polymorphism (SRAP) fingerprints of burdock have all been reported. To make better use of this data for further research and analysis, a burdock database was constructed. RESULTS: This burdock multi-omics database contains two burdock genome datasets, two transcriptome datasets, eight burdock chloroplast genomes, one burdock mitochondrial genome, one A. tomentosum chloroplast genome, one A. tomentosum mitochondrial genome, 26 phenotypes of burdock varieties, burdock rhizosphere-associated microorganisms, and chemical constituents of burdock fruit, pericarp, and kernel at different growth stages (using UPLC-Q-TOF-MS). The wild and cultivation distribution of burdock in China was summarized, and the main active components and pharmacological effects of burdock currently reported were concluded. The database contains ten central functional modules: Home, Genome, Transcriptome, Jbrowse, Search, Tools, SRAP fingerprints, Associated microorganisms, Chemical, and Publications. Among these, the "Tools" module can be used to perform sequence homology alignment (Blast), multiple sequence alignment analysis (Muscle), homologous protein prediction (Genewise), primer design (Primer), large-scale genome analysis (Lastz), and GO and KEGG enrichment analyses (GO Enrichment and KEGG Enrichment). CONCLUSIONS: The database URL is http://210.22.121.250:41352/ . This burdock database integrates molecular and chemical data to provide a comprehensive information and analysis platform for interested researchers and can be of immense help to the cultivation, breeding, and molecular pharmacognosy research of burdock.

Complete chloroplast genome of Ligularia biceps Kitam, 1941 (Asteraceae).

Ligularia biceps is a plant belonging to Ligularia Cass., most of which have certain medicinal value. In this study, the chloroplast (cp) genome of L. biceps was sequenced for the first time. The L. biceps cp genome sequence length was 151,153 bp, with an large single-copy (LSC) region length of 83,259 bp, an small single-copy (SSC) region length of 18,234 bp, a pair of inverted repeat regions (IRs) length of 24,830 bp and GC content of 37.5%. In total, 131 genes were annotated, including 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. The phylogenetic tree was built based on 23 species, using the maximum-likelihood method. The results showed that the species clustered with other Ligularia Cass. species. This study provides a theoretical basis for establishing a classification system.

The complete chloroplast genome of Dictamnus dasycarpus Turcz. (Rutaceae).

Dictamnus dasycarpus Turcz. 1842 is a medicinal plant of China. Its dry root bark is called BAIXIANPI, which is a common traditional Chinese medicine. Here, we report the complete chloroplast genome of D. dasycarpus. The length of the genome, large single-copy (LSC), small single-copy (SSC), inverted repeat (IR), and GC content was 157,056 bp, 84,497 bp, 18,487 bp, 27,036 bp, and 38.5%, respectively. A total of 132 genes were annotated, including 87 protein coding, eight rRNA, and 37 tRNA genes. Interestingly, 15 genes contained single intron while two others contained two introns. The phylogenetic tree showed the two D. dasycarpus (D. albus) clustered in a clade, which was sister to clade formed by the species of Melicope, Tetradium, Phellodendron, and Zanthoxylum.

The complete chloroplast genome of Pulsatilla campanella Fischer ex Krylov. (Ranunculaceae, Pulsatilla Miller).

The complete chloroplast genome of Pulsatilla campanella Fischer ex Krylov was sequenced and reported for the first time. The length of the entire circular genome was 162,322 bp, and the GC content was 37.4%. There were 133 genes annotated, including 89 known protein-coding genes, 36 tRNAs, and 8 rRNAs. The complete chloroplast genome of P.campanella has consisted of two inverted repeat regions (IRs), a large single-copy region (LSC 82,087 bp), and a small single-copy region (SSC 17,497 bp). The phylogenetic tree was built based on 29 species, using the maximum-likelihood method. The results showed that P.campanella was clustered on the same branch with a variety of Pulsatilla plants. The data reveal the genetic relationship between the selected species and provide information for subsequent plant classification.

A Fluorescent "Turn-On" Clutch Probe for Plasma Cell-Free DNA Identification from Lung Cancer Patients.

Early diagnosis of cancer is of paramount significance for the therapeutic intervention of cancers. Although the detection of circulating cell-free DNA (cfDNA) has emerged as a promising, minimally invasive approach for early cancer diagnosis, there is an urgent need to develop a highly sensitive and rapid method to precisely identify plasma cfDNA from clinical samples. Herein, we report a robust fluorescent "turn-on" clutch probe based on non-emissive QDs-Ru complexes to rapidly recognize EGFR gene mutation in plasma cfDNA from lung cancer patients. In this system, the initially quenched emission of QDs is recovered while the red emission of Ru(II) complexes is switched on. This is because the Ru(II) complexes can specifically intercalate into the double-stranded DNA (dsDNA) to form Ru-dsDNA complexes and simultaneously liberate free QDs from the QDs-Ru complexes, which leads to the occurrence of an overlaid red fluorescence. In short, the fluorescent "turn-on" clutch probe offers a specific, rapid, and sensitive paradigm for the recognition of plasma cfDNA biomarkers from clinical samples, providing a convenient and low-cost approach for the early diagnosis of cancer and other gene-mutated diseases.

The complete chloroplast genome sequence of Convallaria majalis L.

The complete chloroplast genome of an important medicinal plant, Convallaria majalis Linnaeus, was sequenced for the first time. The entire circular genome is 162,218 bp in length, with 37.9% GC contents. The genome has consisted of a large single-copy region (LSC) with a length of 85,417 bp, a small single-copy region (SSC) with a length of 18,495 bp, and two inverted repeat regions (IRs) with a length of 29,153 bp each. The genome harbored 133 genes, including 87 protein coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic tree of 24 plant species was constructed based on the maximum-likelihood method. This study will provide theoretical basis for further study on plant genetics phylogenetic research.

The complete chloroplast genome sequence of Veratrum nigrum L.

The complete chloroplast genome of an important medicinal plant, Veratrum nigrum Linnaeus, was sequenced. The entire circular genome is 151,580 bp in length, with 37.7% GC contents. The genome has a large single-copy (LSC) region with a length of 81,806 bp, a small single-copy (SSC) region with a length of 17,472 bp, and two inverted repeat regions (IRs) with a length of 26,151 bp. It harbored 131 genes, including 85 protein coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis suggested V. nigrum formed a monophyletic clade with relatively short genetic distance to Veratrum oxysepalum and Veratrum taliense. This study will provide theoretical basis for further study on plant genetics phylogenetic research.

Near-Infrared Thermally Activated Delayed Fluorescence Nanoparticle: A Metal-Free Photosensitizer for Two-Photon-Activated Photodynamic Therapy at the Cell and Small Animal Levels.

Thermally activated delayed fluorescence (TADF) materials with extremely small singlet-triplet energy offsets have opened new horizons for the development of metal-free photosensitizers for photodynamic therapy (PDT) in recent years. However, the exploration of near-infrared (NIR) TADF emitters for efficient two-photon-excited (TPE) PDT is still a formidable challenge, thus it has not been reported yet. In this study, purely organic photosensitizers (PSs) based on the TADF nanoparticles (NIR-TADF NPs) are designed for efficient TPE-PDT, which show excellent singlet oxygen generation ability. Thanks to the intrinsic two-photon excitation and NIR emission characteristics, the NIR-TADF NPs demonstrate promising potential in both single-photon-excited (SPE) and TPE NIR imaging. More importantly, the anti-tumor efficiency and biosafety of TADF-based PSs at the small animal level are confirmed in A549 tumor xenograft models under TPE laser irradiance, which will facilitate the practical biomedical applications of TADF materials. This work not only provides a promising strategy to develop metal-free PSs, but also expands the applied scope of TADF-based nanotherapeutics and advances their possible clinical translation in cancer therapy.

The first high-quality chromosomal genome assembly of a medicinal and edible plant Arctium lappa.

Arctium lappa has a long medicinal and edible history with great economic importance. Here, the first high-quality chromosome-level draft genome of A. lappa was presented by the Illumina and PacBio sequencing data. The assembled genome was approximately 1.79 Gb with a N50 contig size of 6.88 Mb. Approximately 1.70 Gb (95.4%) of the contig sequences were anchored onto 18 chromosomes using Hi-C data; the scaffold N50 was improved to be 91.64 Mb. Furthermore, we obtained 1.12 Gb (68.46%) of repetitive sequences and 32,771 protein-coding genes; 616 positively selected candidate genes were identified. Among candidate genes related to lignan biosynthesis, the following were found to be highly correlated with the accumulation of arctiin: 4-coumarate-CoA ligase (4CL), dirigent protein (DIR), and hydroxycinnamoyl transferase (HCT). Additionally, we compared the transcriptomes of A. lappa roots at three different developmental stages and identified 8,943 differentially expressed genes (DEGs) in these tissues. These data can be utilized to identify genes related to A. lappa quality or provide a basis for molecular identification and comparative genomics among related species.

Thermally Activated Delayed Fluorescence Material: An Emerging Class of Metal-Free Luminophores for Biomedical Applications.

The development of simple, efficient, and biocompatible organic luminescent molecules is of great significance to the clinical transformation of biomaterials. In recent years, purely organic thermally activated delayed fluorescence (TADF) materials with an extremely small single-triplet energy gap (ΔEST ) have been considered as the most promising new-generation electroluminescence emitters, which is an enormous breakthrough in organic optoelectronics. By merits of the unique photophysical properties, high structure flexibility, and reduced health risks, such metal-free TADF luminophores have attracted tremendous attention in biomedical fields, including conventional fluorescence imaging, time-resolved imaging and sensing, and photodynamic therapy. However, there is currently no systematic summary of the TADF materials for biomedical applications, which is presented in this review. Besides a brief introduction of the major developments of TADF material, the typical TADF mechanisms and fundamental principles on design strategies of TADF molecules and nanomaterials are subsequently described. Importantly, a specific emphasis is placed on the discussion of TADF materials for various biomedical applications. Finally, the authors make a forecast of the remaining challenges and future developments. This review provides insightful perspectives and clear prospects towards the rapid development of TADF materials in biomedicine, which will be highly valuable to exploit new luminescent materials.

The complete mitochondrial genome of Dryopteris crassirhizoma Nakai (Dryopteridaceae, Dryopteris Adanson).

The complete mitochondrial genome of Dryopteris crassirhizoma was sequenced for the first time. The mitochondrial genome length was 313,346 bp, with 48.58% GC contents. There were 94 genes annotated, including 27 known protein-coding genes, 49 tRNAs, and 18 rRNAs. The maximum likelihood method was used to establish the phylogenetic tree of six species. The phylogenetic results showed that D. crassirhizoma was sister to Ophioglossum californicum. It reveals the genetic relationship between different species and provides a theoretical basis for the establishment of a classification system.

The complete mitochondrial genome of Aucklandia lappa Decne. (Asteraceae, Aucklandia Falc.).

The complete mitochondrial genome of Aucklandia lappa was sequenced for the first time. The mitochondrial genome length was 320,439 bp, with 45.05% GC contents. There were 67 genes annotated, including 31 known protein-coding genes, 25 tRNAs, and six rRNAs. The maximum likelihood method was used to establish the phylogenetic tree of 37 species. Results have shown that A. lappa and Arctium lappa were sister groups. It reveals the genetic relationship between different species and provides a theoretical basis for the establishment of a classification system.