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"Yang, Heyu"
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Mitochondrial Genome Sequence of Salvia officinalis (Lamiales: Lamiaceae) Suggests Diverse Genome Structures in Cogeneric Species and Finds the Stop Gain of Genes through RNA Editing Events
Our previous study was the first to confirm that the predominant conformation of mitochondrial genome (mitogenome) sequence of Salvia species contains two circular chromosomes. To further understand the organization, variation, and evolution of Salvia mitogenomes, we characterized the mitogenome of Salvia officinalis. The mitogenome of S. officinalis was sequenced using Illumina short reads and Nanopore long reads and assembled using a hybrid assembly strategy. We found that the predominant conformation of the S. officinalis mitogenome also had two circular chromosomes that were 268,341 bp (MC1) and 39,827 bp (MC2) in length. The S. officinalis mitogenome encoded an angiosperm-typical set of 24 core genes, 9 variable genes, 3 rRNA genes, and 16 tRNA genes. We found many rearrangements of the Salvia mitogenome through inter- and intra-specific comparisons. A phylogenetic analysis of the coding sequences (CDs) of 26 common protein-coding genes (PCGs) of 11 Lamiales species and 2 outgroup taxa strongly indicated that the S. officinalis was a sister taxon to S. miltiorrhiza, consistent with the results obtained using concatenated CDs of common plastid genes. The mapping of RNA-seq data to the CDs of PCGs led to the identification of 451 C-to-U RNA editing sites from 31 PCGs of the S. officinalis mitogenome. Using PCR amplification and Sanger sequencing methods, we successfully validated 113 of the 126 RNA editing sites from 11 PCGs. The results of this study suggest that the predominant conformation of the S. officinalis mitogenome are two circular chromosomes, and the stop gain of rpl5 was found through RNA editing events of the Salvia mitogenome.
Journal Article
Unveiling the mitochondrial genome of Salvia splendens insights into the evolutionary traits within the genus Salvia
Previously, we resolved the complete sequences of the mitochondrial genomes (mitogenome) of two
Salvia
species (
S. miltiorrhiza
and
S. officinalis
). The major configurations of these two species were two circular chromosomes. In this study, we further studied the mitogenome of a floral species of
Salvia
(
Salvia splendens
) to understand the diversity and evolution of the
Salvia
mitogenomes. We sequenced the total DNAs of
S. splendens
using the Nanopore and Illumina platforms and assembled the mitogenome using a hybrid assembly strategy. The major configurations of the
S. splendens
were two circular chromosomes with lengths of 182,239 and 165,055 bp. There were 32 protein-coding genes (PCGs), three rRNA genes, and 18 tRNA genes annotated in the
S. splendens
mitogenome. We found 56 pairs of repetitive sequences in the
S. splendens
mitogenome. Three of them (R01, 04, and 07) could mediate recombination, whose products could be identified by the mapping of Nanopore reads, PCR amplifications, and Sanger sequencing of the PCR products. 457 RNA editing sites were identified in the
S. splendens
mitochondrial RNAs when comparing the RNA-seq data with their corresponding DNA templates. We showed that
S. splendens
was a sister taxon to
S. miltiorrhiza
based on the mitogenomes, consistent with the phylogeny determined with the plastome sequences. Crucially, we developed 12 mitochondrial markers sourced from mitochondrial intron regions to facilitate the identification of three
Salvia
species. Our study offers a comprehensive view of the structure of the
Salvia
mitogenomes and provides robust mitochondrial markers for
Salvia
species identification.
Journal Article
Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences
Background
Alpinia
species are widely used as medicinal herbs. To understand the taxonomic classification and plastome evolution of the medicinal
Alpinia
species and correctly identify medicinal products derived from
Alpinia
species, we systematically analyzed the plastome sequences from five
Alpinia
species. Four of the
Alpinia
species:
Alpinia galanga
(L.) Willd.,
Alpinia hainanensis
K.Schum.,
Alpinia officinarum
Hance, and
Alpinia oxyphylla
Miq., are listed in the Chinese pharmacopeia. The other one,
Alpinia nigra
(Gaertn.) Burtt, is well known for its medicinal values.
Results
The four
Alpinia
species:
A. galanga
,
A. nigra
,
A. officinarum
, and
A. oxyphylla
, were sequenced using the Next-generation sequencing technology. The plastomes were assembled using Novoplasty and annotated using CPGAVAS2. The sizes of the four plastomes range from 160,590 bp for
A. galanga
to 164,294 bp for
A. nigra
, and display a conserved quadripartite structure. Each of the plastomes encodes a total of 111 unique genes, including 79 protein-coding, 28 tRNA, and four rRNA genes. In addition, 293–296 SSRs were detected in the four plastomes, of which the majority are mononucleotides Adenine/Thymine and are found in the noncoding regions. The long repeat analysis shows all types of repeats are contained in the plastomes, of which palindromic repeats occur most frequently. The comparative genomic analyses revealed that the pair of the inverted repeats were less divergent than the single-copy region. Analysis of sequence divergence on protein-coding genes showed that two genes (
acc
D and
ycf
1) had undergone positive selection. Phylogenetic analysis based on coding sequence of 77 shared plastome genes resolves the molecular phylogeny of 20 species from Zingiberaceae. In particular, molecular phylogeny of four sequenced
Alpinia
species (
A. galanga
,
A. nigra
,
A. officinarum
, and
A. oxyphylla
) based on the plastome and nuclear sequences showed congruency. Furthermore, a comparison of the four newly sequenced
Alpinia
plastomes and one previously reported
Alpinia
plastomes (accession number: NC_048461) reveals 59 highly divergent intergenic spacer regions. We developed and validated two molecular markers Alpp and Alpr, based on two regions:
pet
N-
psb
M and
psa
J-
rpl
33, respectively. The discrimination success rate was 100 % in validation experiments.
Conclusions
The results from this study will be invaluable for ensuring the effective and safe uses of
Alpinia
medicinal products and for the exploration of novel
Alpinia
species to improve human health.
Journal Article
Effects of iron oxide nanoparticles as T 2 -MRI contrast agents on reproductive system in male mice
Iron oxide nanoparticles (IONPs)-based contrast agents are widely used for T
-weighted magnetic resonance imaging (MRI) in clinical diagnosis, highlighting the necessity and importance to evaluate their potential systematic toxicities. Although a few previous studies have documented the toxicity concerns of IONPs to major organs, limited data are available on the potential reproductive toxicity caused by IONPs, especially when administrated via intravenous injection to mimic clinical use of MRI contrast agents. Our study aimed to determine whether exposure to IONPs would affect male reproductive system and cause other related health concerns in ICR mice. The mice were intravenously injected with different concentrations IONPs once followed by routine toxicity tests of major organs and a series of reproductive function-related analyses at different timepoints. As a result, most of the contrast agents were captured by reticuloendothelial system (RES) organs such as liver and spleen, while IONPs have not presented adverse effects on the normal function of these major organs. In contrast, although IONPs were not able to enter testis through the blood testicular barrier (BTB), and they have not obviously impaired the overall testicular function or altered the serum sex hormones levels, IONPs exposure could damage Sertoli cells in BTB especially at a relative high concentration. Moreover, IONPs administration led to a short-term reduction in the quantity and quality of sperms in a dose-dependent manner, which might be attributed to the increase of oxidative stress and apoptotic activity in epididymis. However, the semen parameters have gradually returned to the normal range within 14 days after the initial injection of IONPs. Collectively, these results demonstrated that IONPs could cause reversible damage to the reproductive system of male mice without affecting the main organs, providing new guidance for the clinical application of IONPs as T
-MRI contrast agents.
Journal Article
Proteomic analysis of spinal cord tissue in a rat model of cancer-induced bone pain
Cancer-induced bone pain (CIBP) is a moderate to severe pain and seriously affects patients' quality of life. Spinal cord plays critical roles in pain generation and maintenance. Identifying differentially expressed proteins (DEPs) in spinal cord is essential to elucidate the mechanisms of cancer pain.
CIBP rat model was established by the intratibial inoculation of MRMT-1 cells. Positron emission tomography (PET) scan and transmission electron microscopy (TEM) were used to measure the stats of spinal cord in rats. Label free Liquid Chromatography with tandem mass spectrometry (LC-MS-MS) were used to analyze the whole proteins from the lumbar spinal cord. Differentially expressed proteins (DEPs) were performed using Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, and verified using Western blot and immunofluorescence assay.
In the current study, CIBP rats exhibited bone damage, spontaneous pain, mechanical hyperalgesia, and impaired motor ability. In spinal cord, an hypermetabolism and functional abnormality were revealed on CIBP rats. An increase of synaptic vesicles density in active zone and a disruption of mitochondrial structure in spinal cord of CIBP rats were observed. Meanwhile, 422 DEPs, consisting of 167 up-regulated and 255 down-regulated proteins, were identified among total 1539 proteins. GO enrichment analysis indicated that the DEPs were mainly involved in catabolic process, synaptic function, and enzymic activity. KEGG pathway enrichment analysis indicated a series of pathways, including nervous system disease, hormonal signaling pathways and amino acid metabolism, were involved. Expression change of synaptic and mitochondrial related protein, such as complexin 1 (CPLX1), synaptosomal-associated protein 25 (SNAP25), synaptotagmin 1 (SYT1), aldehyde dehydrogenase isoform 1B1 (ALDH1B1), Glycine amidinotransferase (GATM) and NADH:ubiquinone oxidoreductase subunit A11 (NDUFA11), were further validated using immunofluorescence and Western blot analysis.
This study provides valuable information for understanding the mechanisms of CIBP, and supplies potential therapeutic targets for cancer pain.
Journal Article
Distinct transgenic effects of poplar TDIF genes on vascular development in Arabidopsis
Key message
Poplar CLE genes encoding TDIF motifs differentially regulate vascular cambial cell division and woody tissue organization in transgenic
Arabidopsis
.
In
Arabidopsis, CLE41
and
CLE44
genes encode the tracheary element differentiation inhibitory factor (TDIF) peptide, which functions as a non-cell autonomous signal to regulate vascular development, and overexpression of
AtCLE41
/
CLE44
generate similar phenotypic defects. In poplar, there are six
CLE
genes
(PtTDIF1-4
and
PtTDIF-like1-2
) encoding two TDIF peptides (TDIF and TDIF-like peptide), which exhibit nearly same activities when exogenously applied to
Arabidopsis
seedlings. In this work, for each TDIF peptide, we chose two poplar
CLE
genes (
PtTDIF2
and
3
for TDIF, and
PtTDIF-like1-2
for TDIF-like peptide) to compare their in vivo effects in transgenic
Arabidopsis
. Our results showed that transgenic
Arabidopsis
lines overexpressing each individual
PtTDIF
gene exhibited dramatically distinct phenotypes associated with vascular development, demonstrating that TDIF motif is not the only functional determinant after genetic transformation. Moreover, we revealed that overexpressed poplar
TDIFs
enhanced the proliferation of (pro)cambial cells only in hypocotyls, but not in inflorescence stems by differentially regulating the transcriptional levels of
WOX4
and
WOX14
in these two tissues.
Journal Article
The chloroplast genome of the Iris japonica Thunberg (Butterfly flower) reveals the genomic and evolutionary characteristics of Iris species
Iris japonica Thunberg is one of the horticultural species belonging to the Iris genus and Iridaceae family. Previous studies have revealed its hepatoprotective activity and ornamental values. However, little genetic and genomic information about this species is available. Here, to decipher the chloroplast genome and reveal its evolutionary characteristics, we sequenced, de novo assembled, and comprehensively analyzed the chloroplast genome of I. japonica. The genome was 152,453 bp in length and displayed a circular structure with a large single-copy region, a small single-copy region, and two inverted repeat regions. It contained 131 genes, including 85 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. We also identified 23 microsatellite repeat sequences, 34 tandem repeat sequences, and 60 dispersed repeat sequences in the chloroplast genome of I. japonica. Sequence divergence analyses of the chloroplast genomes of 20 Iris species revealed that the top four most highly variable regions were ndhC-trnV-UAC, rpl22-rps19, rps16-trnQ-UUG, and trnG-UCC-trnR-UCU. Phylogenetic analysis showed that I. japonica was most closely related to I. tectorum. This study reported a new chloroplast genome of I. japonica and performed comparative analyses of 20 Iris chloroplast genomes. The results would facilitate the evolutionary research and development of molecular markers for Iris species.
Journal Article
Multifunctional nanozymes: for cancer diagnosis, treatment and monitoring
Natural enzymes are often constrained by high production costs, susceptibility to denaturation and inactivation, and low yields, all of which limit their widespread application. As an emerging class of artificial enzymes, nanozymes, which integrate the properties of nanomaterials and enzymes, have attracted increasing attention as promising alternatives. Multifunctional nanozymes, defined as nanomaterials possessing enzyme like catalytic activities, exhibit considerable potential in tumor theranostics due to their high stability, tunable catalytic performance, and favorable biocompatibility. This review systematically summarizes the classification of nanozymes and their applications in tumor diagnosis, therapy, and monitoring. In diagnostics, nanozymes enable highly sensitive in vitro detection of biomarkers such as circulating tumor cells (CTCs), ctDNA, and miRNAs, and facilitate precise tumor localization and real-time monitoring in vivo through multimodal imaging modalities including fluorescence, magnetic resonance, and photoacoustic imaging. In therapeutics, by mimicking the activities of peroxidase (POD), oxidase (OXD), catalase (CAT), and superoxide dismutase (SOD), nanozymes participate in diverse treatment strategies such as cascade catalytic reactions, immunomodulation, photodynamic therapy (PDT) and sonodynamic therapy (SDT), photothermal therapy (PTT), and starvation therapy, as shown in Scheme
1
. These approaches effectively modulate the tumor microenvironment (TME), enhance treatment specificity, and reduce side effects. Although significant progress in nanozyme based tumor theranostics, challenges remain, including insufficient catalytic specificity, limited in vivo targeting efficiency, unclear long-term biosafety, and the lack of mature large-scale manufacturing processes. Future efforts should prioritize biomimetic design, material optimization, multimodal synergy, and clinical translation to further advance nanozymes toward a precise, efficient, and safe platform for tumor diagnosis and therapy.
Journal Article
Biomimetic nanozymes for tumor diagnosis and treatment
As a major global health threat, cancer continues to pose significant challenges for diagnosis and treatment. Nanozymes are nanomaterials that mimic the catalytic functions of natural enzymes while offering high stability and tunable activity, thereby providing a novel perspective for cancer theranostics. This review systematically describes the classification and catalytic properties of nanozymes. It further highlights biomimetic design strategies based on exosomes, leveraging their inherent targeting and penetration capabilities to enhance the delivery efficiency of nanozymes to tumor tissues. In diagnosis, nanozymes enable sensitive detection and multi-modal imaging of tumor biomarkers and cells through catalytic chromogenic reactions and signal amplification. In therapy, nanozymes exert specific therapeutic effects within the tumor microenvironment (TME) via diverse mechanisms such as catalytic therapy, cascade reactions, starvation therapy, radiosensitization, gas therapy, and immunomodulation. Despite current challenges including biosafety, limited targeting specificity, restricted catalytic diversity, and barriers to clinical translation, further optimization of biomimetic designs and promotion of clinical translation may support the development of safer and more efficient nanozyme-based strategies for cancer diagnosis and treatment.
Journal Article