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1.
Talanta ; 279: 126601, 2024 Jul 22.
Article in English | MEDLINE | ID: mdl-39079435

ABSTRACT

Single gas quantification and mixed gas identification have been the major challenges in the field of gas detection. To address the shortcomings of chemo-resistive gas sensors, sensor arrays have been the subject of recent research. In this work, the research focused on both optimization of gas-sensing materials and further analysis of pattern recognition algorithms. Four bimetallic oxide-based gas sensors capable of operating at room temperature were first developed by introducing different modulating techniques on the sensing layer, including constructing surface oxygen defects, polymerizing conducting polymers, modifying Nano-metal, and compositing flexible substrates. The signals derived from the gas sensor array were then processed to eliminate noise and reduce dimension with the feature engineering. The gases of were qualitatively identified by support vector machine (SVM) model with an accuracy of 98.86 %. Meanwhile, a combined model of convolutional neural network and long short-term memory network (CNN-LSTM) was established to remove the interference samples and quantitatively estimate the concentration of the target gases. The combined model based on deep learning, which avoids the overfitting with local optimal solutions, effectively boosts the performance of concentration recognition with the lowest root mean square error (RMSE) of 2.3. Finally, a low-power artificial olfactory system was established by merging the multi-sensor data and applied for real-time and accurate judgment of the food freshness.

2.
Molecules ; 29(14)2024 Jul 17.
Article in English | MEDLINE | ID: mdl-39064926

ABSTRACT

Molybdenum (Mo) is a rare and important element extensively utilised in aerospace, radar communications, optoelectronic devices, and the military. This study proposes an environmentally friendly physical method based on photon-phonon resonance absorption for the separation of Mo from sodium molybdate (Na2MoO4). We examined the vibrational spectrum of Na2MoO4 using the CASTEP code, employing first-principles density functional theory. Through dynamic process analysis, we analysed the vibrational modes and assigned peaks corresponding to experimental infrared (IR) and Raman data. We focused on the vibrational modes associated with Mo and identified that the highest-intensity IR-active peak at 858 cm-1 corresponded to Mo-O bond asymmetric stretching. Therefore, we propose the use of a high-power terahertz laser at ~25 THz to facilitate the separation of Mo from Na2MoO4. Experimental investigations are expected in the future.

3.
Br J Cancer ; 131(3): 430-443, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38877108

ABSTRACT

BACKGROUND: Targeting DNA damage repair factors, such as DNA-dependent protein kinase catalytic subunit (DNA-PKcs), may offer an opportunity for effective treatment of multiple myeloma (MM). In combination with DNA damage-inducing agents, this strategy has been shown to improve chemotherapies partially via activation of cGAS-STING pathway by an elevated level of cytosolic DNA. However, as cGAS is primarily sequestered by chromatin in the nucleus, it remains unclear how cGAS is released from chromatin and translocated into the cytoplasm upon DNA damage, leading to cGAS-STING activation. METHODS: We examined the role of DNA-PKcs inhibition on cGAS-STING-mediated MM chemosensitivity by performing mass spectrometry and mechanism study. RESULTS: Here, we found DNA-PKcs inhibition potentiated DNA damage-inducing agent doxorubicin-induced anti-MM effect by activating cGAS-STING signaling. The cGAS-STING activation in MM cells caused cell death partly via IRF3-NOXA-BAK axis and induced M1 polarization of macrophages. Moreover, this activation was not caused by defective classical non-homologous end joining (c-NHEJ). Instead, upon DNA damage induced by doxorubicin, inhibition of DNA-PKcs promoted cGAS release from cytoplasmic chromatin fragments and increased the amount of cytosolic cGAS and DNA, activating cGAS-STING. CONCLUSIONS: Inhibition of DNA-PKcs could improve the efficacy of doxorubicin in treatment of MM by de-sequestrating cGAS in damaged chromatin.


Subject(s)
Chromatin , DNA Damage , DNA-Activated Protein Kinase , Doxorubicin , Membrane Proteins , Multiple Myeloma , Nucleotidyltransferases , Humans , Multiple Myeloma/drug therapy , Multiple Myeloma/pathology , Multiple Myeloma/metabolism , Multiple Myeloma/genetics , Nucleotidyltransferases/metabolism , Nucleotidyltransferases/genetics , DNA-Activated Protein Kinase/metabolism , DNA-Activated Protein Kinase/antagonists & inhibitors , Chromatin/metabolism , Chromatin/drug effects , DNA Damage/drug effects , Doxorubicin/pharmacology , Membrane Proteins/metabolism , Membrane Proteins/genetics , Cell Line, Tumor , Mice , Animals , Signal Transduction/drug effects
4.
Plants (Basel) ; 13(12)2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38931077

ABSTRACT

Photosynthetic induction and stomatal kinetics are acknowledged as pivotal factors in regulating both plant growth and water use efficiency under fluctuating light conditions. However, the considerable variability in methodologies and light regimes used to assess the dynamics of photosynthesis (A) and stomatal conductance (gs) during light induction across studies poses challenges for comparison across species. Moreover, the influence of stomatal morphology on both steady-state and non-steady-state gs remains poorly understood. In this study, we show the strong impact of IRGA Chamber Illumination and Whole Plant Illumination on the photosynthetic induction of two rice species. Our findings reveal that these illuminations significantly enhance photosynthetic induction by modulating both stomatal and biochemical processes. Moreover, we observed that a higher density of smaller stomata plays a critical role in enhancing the stomatal opening and photosynthetic induction to fluctuating light conditions, although it exerts minimal influence on steady-state gs and A under constant light conditions. Therefore, future studies aiming to estimate photosynthetic induction and stomatal kinetics should consider the light environments at both the leaf and whole plant levels.

5.
J Parkinsons Dis ; 14(4): 833-842, 2024.
Article in English | MEDLINE | ID: mdl-38728202

ABSTRACT

Background: Previous studies have demonstrated the importance of the locus coeruleus (LC) in sleep-wake regulation. Both essential tremor (ET) and Parkinson's disease (PD) share common sleep disorders, such as poor quality of sleep (QoS). LC pathology is a feature of both diseases. A question arises regarding the contribution of LC degeneration to the occurrence of poor QoS. Objective: To evaluate the association between LC impairment and sleep disorders in ET and PD patients. Methods: A total of 83 patients with ET, 124 with PD, and 83 healthy individuals were recruited and divided into ET/PD with/without poor QoS (Sle/NorET and Sle/NorPD) subgroups according to individual Pittsburgh Sleep Quality Index (PSQI) score. Neuromelanin-sensitive magnetic resonance imaging (NM-MRI) and free-water imaging derived from diffusion MRI were performed. Subsequently, we evaluated the association between contrast-to-noise ratio of LC (CNRLC) and free-water value of LC (FWLC) with PSQI scores in ET and PD groups. Results: CNRLC was significantly lower in ET (p = 0.047) and PD (p = 0.018) than in healthy individuals, whereas no significant difference was found in FWLC among the groups. No significant differences were observed in CNR/FWLC between patients with/without sleep disorders after multiple comparison correction. No correlation was identified between CNR/FWLC and PSQI in ET and PD patients. Conclusions: LC degeneration was observed in both ET and PD patients, implicating its involvement in the pathophysiology of both diseases. Additionally, no significant association was observed between LC integrity and PSQI, suggesting that LC impairment might not directly relate to overall QoS.


Subject(s)
Essential Tremor , Locus Coeruleus , Parkinson Disease , Sleep Wake Disorders , Humans , Essential Tremor/physiopathology , Essential Tremor/complications , Essential Tremor/pathology , Locus Coeruleus/diagnostic imaging , Locus Coeruleus/pathology , Female , Male , Parkinson Disease/complications , Parkinson Disease/physiopathology , Parkinson Disease/diagnostic imaging , Aged , Middle Aged , Sleep Wake Disorders/etiology , Sleep Wake Disorders/physiopathology , Magnetic Resonance Imaging , Nerve Degeneration/pathology , Sleep Quality , Melanins
6.
Sci Total Environ ; 934: 173119, 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-38750743

ABSTRACT

Paraquat (PQ) is a broad-spectrum herbicide used worldwide and is a hazardous chemical to human health. Cumulative evidence strengthens the association between PQ exposure and the development of Parkinson's disease (PD). However, the underlying mechanism and effective interventions against PQ-induced neurotoxicity remain unclear. In this study, C57BL/6 J mice were treated with PQ (i.p., 10 mg/kg, twice a week) and melatonin (i.g., 20 mg/kg, twice a week) for 8 weeks. Results showed that PQ-induced motor deficits and midbrain dopaminergic neuronal damage in C57BL/6 J mice were protected by melatonin pretreatment. In isolated primary midbrain neurons and SK-N-SH cells, reduction of cell viability, elevation of total ROS levels, axonal mitochondrial transport defects and mitochondrial dysfunction caused by PQ were attenuated by melatonin. After screening of expression of main motors driving axonal mitochondrial transport, data showed that PQ-decreased KIF5A expression in mice midbrain and in SK-N-SH cell was antagonized by melatonin. Using the in vitro KIF5A-overexpression model, it was found that KIF5A overexpression inhibited PQ-caused neurotoxicity and mitochondrial dysfunction in SK-N-SH cells. In addition, application of MTNR1B (MT2) receptor antagonist, 4-P-PDOT, significantly counteracted the protection of melatonin against PQ-induced neurotoxicity. Further, Kif5a-knockdown diminished melatonin-induced alleviation of motor deficits and neuronal damage against PQ in C57BL/6 J mice. The present study establishes a causal link between environmental neurotoxicants exposure and PD etiology and provides effective interventive targets in the pathogenesis of PD.


Subject(s)
Kinesins , Melatonin , Mesencephalon , Mice, Inbred C57BL , Mitochondria , Paraquat , Paraquat/toxicity , Animals , Melatonin/pharmacology , Mice , Mesencephalon/drug effects , Mesencephalon/metabolism , Kinesins/metabolism , Mitochondria/drug effects , Mitochondria/metabolism , Herbicides/toxicity , Neurons/drug effects , Dopaminergic Neurons/drug effects , Axonal Transport/drug effects
7.
J Adv Res ; 2024 Apr 13.
Article in English | MEDLINE | ID: mdl-38614215

ABSTRACT

INTRODUCTION: Senescence refers to a state of permanent cell growth arrest and is regarded as a tumor suppressive mechanism, whereas accumulative evidence demonstrate that senescent cells play an adverse role during cancer progression. The scarcity of specific and reliable markers reflecting senescence level in cancer impede our understanding of this biological basis. OBJECTIVES: Senescence-related genes (SRGs) were collected for integrative analysis to reveal the role of senescence in hepatocellular carcinoma (HCC). METHODS: Consensus clustering was used to subtype HCC based on SRGs. Several computational methods, including single sample gene set enrichment analysis (ssGSEA), fuzzy c-means algorithm, were performed. Data of drug sensitivities were utilized to screen potential therapeutic agents for different senescence patients. Additionally, we developed a method called signature-related gene analysis (SRGA) for identification of markers relevant to phenotype of interest. Experimental strategies consisting quantitative real-time PCR (qRT-PCR), ß-galactosidase assay, western blot, and tumor-T cell co-culture system were used to validate the findings in vitro. RESULTS: We identified three robust prognostic clusters of HCC patients with distinct survival outcome, mutational landscape, and immune features. We further extracted signature genes of senescence clusters to construct the senescence scoring system and profile senescence level in HCC at bulk and single-cell resolution. Senescence-induced stemness reprogramming was confirmed both in silico and in vitro. HCC patients with high senescence were immune suppressed and sensitive to Tozasertib and other drugs. We suggested that MAFG, PLIN3, and 4 other genes were pertinent to HCC senescence, and MAFG potentially mediated immune suppression, senescence, and stemness. CONCLUSION: Our findings provide insights into the role of SRGs in patients stratification and precision medicine.

8.
ACS Omega ; 9(9): 10517-10521, 2024 Mar 05.
Article in English | MEDLINE | ID: mdl-38463289

ABSTRACT

Tungsten (W) is an extremely rare and vital metal extensively used in metallurgy, the chemical industry, optoelectronic devices, and machinery manufacturing. In this work, an environmentally friendly and efficient physical method based on photon-phonon resonance absorption (PPRA) is proposed for separating W from scheelite. We calculated the vibrational spectrum of calcium tungstate (CaWO4) and assigned the infrared (IR) absorption and Raman scattering peaks through a dynamic analysis of the normal modes. We focused on the strong IR absorption peaks related to W and identified three high-intensity IR-active modes at around 830 cm-1, corresponding to the stretching of the W-O bonds. Therefore, we propose the use of high-power terahertz (∼25 THz) laser radiation to facilitate W extraction from compounds, leveraging the high efficiency of PPRA. Experimental testing is required to determine the precise absorption frequency under industrial production conditions.

9.
Front Bioeng Biotechnol ; 12: 1329712, 2024.
Article in English | MEDLINE | ID: mdl-38515621

ABSTRACT

The failure of endogenous repair is the main feature of neurological diseases that cannot recover the damaged tissue and the resulting dysfunction. Currently, the range of treatment options for neurological diseases is limited, and the approved drugs are used to treat neurological diseases, but the therapeutic effect is still not ideal. In recent years, different studies have revealed that neural stem cells (NSCs) have made exciting achievements in the treatment of neurological diseases. NSCs have the potential of self-renewal and differentiation, which shows great foreground as the replacement therapy of endogenous cells in neurological diseases, which broadens a new way of cell therapy. The biological functions of NSCs in the repair of nerve injury include neuroprotection, promoting axonal regeneration and remyelination, secretion of neurotrophic factors, immune regulation, and improve the inflammatory microenvironment of nerve injury. All these reveal that NSCs play an important role in improving the progression of neurological diseases. Therefore, it is of great significance to better understand the functional role of NSCs in the treatment of neurological diseases. In view of this, we comprehensively discussed the application and value of NSCs in neurological diseases as well as the existing problems and challenges.

10.
ACS Omega ; 9(1): 988-993, 2024 Jan 09.
Article in English | MEDLINE | ID: mdl-38222501

ABSTRACT

Tantalum (Ta) is a valuable and rare metal that is extensively used in the production of implant materials and high-performance capacitors. However, a convenient and effective method for the separation of Ta from other compounds has yet to be developed. On the basis of first-principle density functional theory (DFT), we simulated the vibrational spectrum of potassium heptafluorotantalate (K2TaF7). By performing a dynamics analysis of vibrational modes, we assigned peaks in infrared (IR) absorption and Raman scattering spectra to their corresponding vibrations. We focused on the strong IR absorption peaks of Ta-related vibrational modes in K2TaF7 and concluded that three observed IR absorption peaks, at 285, 315, and 530 cm-1, are good candidates. Provided with high power radiation at these three frequencies (at about 8.55, 9.45, and 15.9 THz), the good efficiency of photon-phonon resonance absorption will facilitate Ta separation from a compound.

11.
Eur J Pharmacol ; 966: 176346, 2024 Mar 05.
Article in English | MEDLINE | ID: mdl-38246329

ABSTRACT

Cell transplantation has brought about a breakthrough in the treatment of nerve injuries, and the efficacy of cell transplantation compared to drug and surgical therapies is very exciting. In terms of transplantation targets, the classic cells include neural stem cells (NSCs) and Schwann cells, while a class of cells that can exist and renew throughout the life of the nervous system - olfactory ensheathing cells (OECs) - has recently been discovered in the olfactory system. OECs not only encircle the olfactory nerves but also act as macrophages and play an innate immune role. OECs can also undergo reprogramming to transform into neurons and survive and mature after transplantation. Currently, many studies have confirmed the repairing effect of OECs after transplantation into injured nerves, and safe and effective results have been obtained in clinical trials. However, the specific repair mechanism of OECs among them is not quite clear. For this purpose, we focus here on the repair mechanisms of OECs, which are summarized as follows: neuroprotection, secretion of bioactive factors, limitation of inflammation and immune regulation, promotion of myelin and axonal regeneration, and promotion of vascular proliferation. In addition, integrating the aspects of harvesting, purification, and prognosis, we found that OECs may be more suitable for transplantation than NSCs and Schwann cells, but this does not completely discard the value of these classical cells. Overall, OECs are considered to be one of the most promising transplantation targets for the treatment of nerve injury disorders.


Subject(s)
Neural Stem Cells , Spinal Cord Injuries , Humans , Olfactory Bulb , Myelin Sheath , Neurons , Cell Transplantation/methods , Nerve Regeneration , Neuroglia
12.
Adv Mater ; 36(19): e2305770, 2024 May.
Article in English | MEDLINE | ID: mdl-38108598

ABSTRACT

Recent theoretical investigations have well-predicted strain-induced nonmonotonic optical band gap variations in low-dimensional materials. However, few two-dimensional (2D) materials are experimentally confirmed to exhibit nonmonotonic optical band gap variation under varying strain. Here, a strain-induced nonmonotonic optical bandgap variation in violet phosphorus (VP) nanosheets is observed, as evidenced by photoluminescence spectroscopy, which is reported in a few other 2D materials in knowledge. The optical bandgap variations are characterized to show the modulation rates of 41 and -24 meV/% with compression and tensile strains, respectively. Remarkably, first-principle calculations predict and clarify the nonmonotonic modulation accurately, highlighting its relationship with the strain direction-dependent asymmetric distribution of conduction band minimum wavefunctions, demonstrating that this unique nonmonotonic optical bandgap modulation is determined by the distinctive crystal structure of VP. This work provides a deep insight into the design of 2D materials toward optoelectronic and photoelectrochemical applications via strain engineering.

13.
Sci Rep ; 13(1): 21358, 2023 12 04.
Article in English | MEDLINE | ID: mdl-38049474

ABSTRACT

The clinical significance and comprehensive characteristics of chemokines and chemokine receptors in female patients with advanced colorectal adenocarcinoma have not ever been reported. Our study explored the expression profiles of chemokines and chemokine receptors and constructed a chemokine- and chemokine receptor-based signature in female patients with advanced colorectal adenocarcinoma. Four independent cohorts containing 1335 patients were enrolled in our study. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analyses were performed to construct the signature. CIBERSORT was used to evaluate the landscape of immune cell infiltration. Thirty-two pairs of tissue specimens of female advanced colorectal cancer (CRC) patients and two CRC cell lines were used to validate the signature in vitro. Quantitative real-time PCR and western blotting were performed to validate the mRNA and protein expression levels of signature genes. EdU and colony formation assays were performed to examine proliferative ability. Transwell and wound healing assays were used to evaluate cell invasion and migration capacity. During the signature construction and validation process, we found that the signature was more applicable to female patients with advanced colorectal adenocarcinoma. Hence, the subsequent study mainly focused on the particular subgroup. Enrichment analyses revealed that the signature was closely related to immunity. The landscape of immune cell infiltration presented that the signature was significantly associated with T cells CD8 and neutrophils. Gene set enrichment analysis (GSEA) confirmed that the high-risk group was chiefly enriched in the tumor-promoting related pathways and biological processes, whereas the low-risk group was mainly enriched in anti-tumor immune response pathways and biological processes. The signature was closely correlated with CTLA4, PDL1, PDL2, TMB, MSI, and TIDE, indicating that our signature could serve as a robust biomarker for immunotherapy and chemotherapy response. ROC curves verified that our signature had more robust prognostic power than all immune checkpoints and immunotherapy-related biomarkers. Finally, we used 32 pairs of tissue specimens and 2 CRC cell lines to validate our signature in vitro. We first provided a robust prognostic chemokine- and chemokine receptor-based signature, which could serve as a novel biomarker for immunotherapy and chemotherapy response to guide individualized treatment for female patients with advanced colorectal adenocarcinoma.


Subject(s)
Adenocarcinoma , Colorectal Neoplasms , Humans , Female , Adenocarcinoma/genetics , Adenocarcinoma/therapy , Colorectal Neoplasms/genetics , Colorectal Neoplasms/therapy , Immunotherapy , Chemokines/genetics , Receptors, Chemokine , Prognosis
14.
Molecules ; 28(21)2023 Oct 30.
Article in English | MEDLINE | ID: mdl-37959761

ABSTRACT

Cl, Br, and I are elements in the halogen family, and are often used as dopants in semiconductors. When employed as dopants, these halogens can significantly modify the optoelectronic properties of materials. From the perspective of halogen doping, we have successfully achieved the stabilization of crystal structures in CH3NH3PbX3, CH3NH3PbI3-xClx, CH3NH3PbI3-xBrx, and CH3NH3PbBr3-xClx, which are organic-inorganic hybrid perovskites. Utilizing first-principles density functional theory calculations with the CASTEP module, we investigated the optoelectronic properties of these structures by simulations. According to the calculations, a smaller difference in electronegativity between different halogens in doped structures can result in smoother energy bands, especially in CH3NH3PbI3-xBrx and CH3NH3PbBr3-xClx. The PDOS of the Cl-3p orbitals undergoes a shift along the energy axis as a result of variances in electronegativity levels. The optoelectronic performance, carrier mobility, and structural stability of the CH3NH3PbBr3-xClx system are superior to other systems like CH3NH3PbX3. Among many materials considered, CH3NH3PbBr2Cl exhibits higher carrier mobility and a relatively narrower bandgap, making it a more suitable material for the absorption layer in solar cells. This study provides valuable insights into the methodology employed for the selection of specific types, quantities, and positions of halogens for further research on halogen doping.

15.
Mol Ther Nucleic Acids ; 34: 102072, 2023 Dec 12.
Article in English | MEDLINE | ID: mdl-38028195

ABSTRACT

Paired SpCas9 nickases (SpCas9n) are an effective strategy to reduce off-target effect in genome editing. However, this approach is not efficient with 3'-overhanging ends, limiting its applications. In order to expand the utility of paired SpCas9n in genome editing, we tested the effect of the TREX2 3'-5' exonuclease on repair of 3'-overhanging ends. We found ectopic overexpression of Trex2 stimulates the efficiency of paired SpCas9n in genome disruption with 3'-overhanging ends up to 400-fold with little stimulation of off-target editing. TREX2 overexpressed preferentially deletes entire 3' overhangs but has no significant effect on 5' overhangs. Trex2 overexpression also stimulates genome disruption by paired SpCas9n that potentially generate short 3'-overhanging ends at overlapping SpCas9n target sites, suggesting sequential nicking of overlapping target sites by SpCas9n. This approach is further simplified with improved efficiency and safety by fusion of TREX2 and particularly its DNA-binding-deficient mutant to SpCas9n. Junction analysis at overlapping targets revealed the different extent of end resection of 3' single-stranded DNA (ssDNA) by free TREX2 and TREX2 fused to SpCas9n. SpCas9n-TREX2 fusion is more convenient and safer than overexpression of free TREX2 to process 3'-overhanging ends for efficient genome disruption by paired SpCas9n, allowing practical use of this TREX2-based strategy in genome editing.

16.
Int J Nanomedicine ; 18: 5511-5527, 2023.
Article in English | MEDLINE | ID: mdl-37791321

ABSTRACT

Extracellular vesicles (EVs) are small membrane-bound vesicles that are released by cells into the extracellular environment. The role of EVs in tumors has been extensively studied, and they have been shown to play a crucial role in tumor growth, progression, and metastasis. Past research has mainly used 2D-cultured cell line models to investigate the role of EVs in tumors, which poorly simulate the tumor microenvironment. Organoid technology has gradually matured in recent years. Organoids are similar in composition and behavior to physiological cells and have the potential to recapitulate the architecture and function of the original tissue. It has been widely used in organogenesis, drug screening, gene editing, precision medicine and other fields. The integration of EVs and organoids has the potential to revolutionize the field of cancer research and represents a promising avenue for advancing our understanding of cancer biology and the development of novel therapeutic strategies. Here, we aimed to present a comprehensive overview of studies using organoids to study EVs in tumors.


Subject(s)
Extracellular Vesicles , Neoplasms , Humans , Neoplasms/pathology , Extracellular Vesicles/metabolism , Organoids/pathology , Tumor Microenvironment
17.
Genome Med ; 15(1): 80, 2023 10 06.
Article in English | MEDLINE | ID: mdl-37803452

ABSTRACT

BACKGROUND: Primary liver cancer has significant intratumor genetic heterogeneity (IGH), which drives cancer evolution and prevents effective cancer treatment. CRISPR/Cas9-induced mouse liver cancer models can be used to elucidate how IGH is developed. However, as CRISPR/Cas9 could induce chromothripsis and extrachromosomal DNA in cells in addition to targeted mutations, we wondered whether this effect contributes to the development of IGH in CRISPR/Cas9-induced mouse liver cancer. METHODS: CRISPR/Cas9-based targeted somatic multiplex-mutagenesis was used to target 34 tumor suppressor genes (TSGs) for induction of primary liver tumors in mice. Target site mutations in tumor cells were analyzed and compared between single-cell clones and their subclones, between different time points of cell proliferation, and between parental clones and single-cell clones derived from mouse subcutaneous allografts. Genomic instability and generation of extrachromosomal circular DNA (eccDNA) was explored as a potential mechanism underlying the oscillation of target site mutations in these liver tumor cells. RESULTS: After efficiently inducing autochthonous liver tumors in mice within 30-60 days, analyses of CRISPR/Cas9-induced tumors and single-cell clones derived from tumor nodules revealed multiplexed and heterogeneous mutations at target sites. Many target sites frequently displayed more than two types of allelic variations with varying frequencies in single-cell clones, indicating increased copy number of these target sites. The types and frequencies of targeted TSG mutations continued to change at some target sites between single-cell clones and their subclones. Even the proliferation of a subclone in cell culture and in mouse subcutaneous graft altered the types and frequencies of targeted TSG mutations in the absence of continuing CRISPR/Cas9 genome editing, indicating a new source outside primary chromosomes for the development of IGH in these liver tumors. Karyotyping of tumor cells revealed genomic instability in these cells manifested by high levels of micronuclei and chromosomal aberrations including chromosomal fragments and chromosomal breaks. Sequencing analysis further demonstrated the generation of eccDNA harboring targeted TSG mutations in these tumor cells. CONCLUSIONS: Small eccDNAs carrying TSG mutations may serve as an important source supporting intratumor heterogeneity and tumor evolution in mouse liver cancer induced by multiplexed CRISPR/Cas9.


Subject(s)
CRISPR-Cas Systems , Liver Neoplasms , Mice , Animals , Liver Neoplasms/genetics , Gene Editing , Mutation , Genes, Tumor Suppressor , DNA , Genomic Instability , DNA, Circular
18.
Molecules ; 28(17)2023 Aug 28.
Article in English | MEDLINE | ID: mdl-37687114

ABSTRACT

The theory of electron spin has been proposed for a century, but the study of quantum effects in biological molecules is still in its infancy. Chirality-induced spin selectivity (CISS) is a very modern theory that can explain many biochemical phenomena. In this paper, we propose a new theoretical model based on CISS theory and quantum chemistry theory, which can well explain the theoretical explanation of the chiral selectivity of chiral proteins. Moreover, this theory can predict the spin state of corresponding chiral molecules. Taking the L-DOPA and AADC enzymes as examples, this theoretical model elucidates the AADC enzyme's chiral catalysis selectivity and successfully predicts the spin state of L-DOPA and D-DOPA's valence electrons.

19.
Front Plant Sci ; 14: 1234866, 2023.
Article in English | MEDLINE | ID: mdl-37746023

ABSTRACT

Chlorophyll content and fluorescence parameters are crucial indicators to evaluate the light use efficiency in rice; however, the correlations among these parameters and the underlying genetic mechanisms remain poorly understood. Here, to clarify these issues, we conducted a genome-wide association study (GWAS) on 225 rice accessions. In the phenotypic and Mendelian randomization (MR) analysis, a weak negative correlation was observed between the chlorophyll content and actual quantum yield of photosystem II (ΦII). The phenotypic diversity observed in SPAD, NPQt, ΦNPQ, and Fv/Fm among accessions was affected by genetic background. Furthermore, the GWAS identified 78 SNPs and 17 candidate genes significantly associated with SPAD, NPQt, ΦII, ΦNPQ, qL and qP. Combining GWAS on 225 rice accessions with transcriptome analysis of two varieties exhibiting distinct fluorescence characteristics revealed two potential candidate genes (Os03g0583000 from ΦII & qP traits and Os06g0587200 from NPQt trait), which are respectively associated with peroxisomes, and protein kinase catalytic domains might involve in regulating the chlorophyll content and chlorophyll fluorescence. This study provides novel insights into the correlation among chlorophyll content and fluorescence parameters and the genetic mechanisms in rice, and offers valuable information for the breeding of rice with enhanced photosynthetic efficiency.

20.
Molecules ; 28(16)2023 Aug 20.
Article in English | MEDLINE | ID: mdl-37630397

ABSTRACT

Two-dimensional (2D) ice I is atomic-level ice that is composed of two interlocked atomic layers saturated with hydrogen bonds. It has recently been experimentally observed, but its properties have yet to be clarified. Accordingly, we theoretically studied the hydrophobic properties of 2D ice I. On the contrary, a simulation of a hydrogen fluoride molecule on a 2D ice surface manifested that it destroyed the 2D ice structure and connected new hydrogen bonds with water molecules. Investigations of the interfacial effect between 2D and three-dimensional (3D) ice films indicated that the network structure of 2D ice was not destroyed by a 3D ice surface, as the former was saturated with hydrogen bonds. However, the surface of 3D ice reorganized to form as many hydrogen bonds as possible. Thus, the 2D ice film was hydrophobic and inhibited the growth of 3D ice. This shows that if 2D ice can be produced on an industrial scale, it can be used as an anti-3D-icing agent under low temperatures.

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