Extraction and analysis of high-quality chloroplast DNA with reduced nuclear DNA for medicinal plants.

BACKGROUND: Obtaining high-quality chloroplast genome sequences requires chloroplast DNA (cpDNA) samples that meet the sequencing requirements. The quality of extracted cpDNA directly impacts the efficiency and accuracy of sequencing analysis. Currently, there are no reported methods for extracting cpDNA from Erigeron breviscapus. Therefore, we developed a suitable method for extracting cpDNA from E. breviscapus and further verified its applicability to other medicinal plants. RESULTS: We conducted a comparative analysis of chloroplast isolation and cpDNA extraction using modified high-salt low-pH method, the high-salt method, and the NaOH low-salt method, respectively. Subsequently, the number of cpDNA copies relative to the nuclear DNA (nDNA ) was quantified via qPCR. As anticipated, chloroplasts isolated from E. breviscapus using the modified high-salt low-pH method exhibited intact structures with minimal cell debris. Moreover, the concentration, purity, and quality of E. breviscapus cpDNA extracted through this method surpassed those obtained from the other two methods. Furthermore, qPCR analysis confirmed that the modified high-salt low-pH method effectively minimized nDNA contamination in the extracted cpDNA. We then applied the developed modified high-salt low-pH method to other medicinal plant species, including Mentha haplocalyx, Taraxacum mongolicum, and Portulaca oleracea. The resultant effect on chloroplast isolation and cpDNA extraction further validated the generalizability and efficacy of this method across different plant species. CONCLUSIONS: The modified high-salt low-pH method represents a reliable approach for obtaining high-quality cpDNA from E. breviscapus. Its universal applicability establishes a solid foundation for chloroplast genome sequencing and analysis of this species. Moreover, it serves as a benchmark for developing similar methods to extract chloroplast genomes from other medicinal plants.

Synthesis and biological evaluation of 4-imidazolidinone-containing compounds as potent inhibitors of the MDM2/p53 interaction.

Inhibition of MDM2/p53 interaction with small-molecule inhibitors stabilizes p53 from MDM2 mediated degradation, which is a promising strategy for the treatment of cancer. In this report, a novel series of 4-imidazolidinone-containing compounds have been synthesized and tested in MDM2/p53 and MDM4/p53 FP binding assays. Upon SAR studies, compounds 2 (TB114) and 22 were identified as the most potent inhibitors of MDM2/p53 but not MDM4/p53 interactions. Both 2 and 22 exhibited strong antiproliferative activities in HCT-116 and MOLM-13 cell lines harboring wild type p53. Mechanistic studies show that 2 and 22 dose-dependently activated p53 and its target genes and induced apoptosis in cells based on the Western blot, qPCR, and flow cytometry assays. In addition, the antiproliferative activities of 2 and 22 were dependent on wild type p53, while they were not toxic to HEK-293 kidney cells. Furthermore, the on-target activities of 2 were general and applicable to other cancer cell lines with wild type p53. These attributes make 2 a good candidate for future optimization to discover a potential treatment of wild-type p53 cancer.

Enhanced electromagnetic wave absorption properties of SiCN(Ni)/BN ceramics by in situ generated Ni and Ni3Si.

In this paper, the SiCN(Ni)/BN ceramic with excellent electromagnetic wave (EMW) absorption performance was successfully prepared. The Ni and Ni3Si were in situ formed by the introduction of nickel acetylacetonate (NA), which effectively improved the impedance matching performance of SiCN(Ni)/BN ceramics. The EMW absorption properties of the SiCN(Ni)/BN ceramics showed a trend of first increasing and then decreasing with the increase in content of NA. When the NA content reached 7 wt%, the impedance matching range of SiCN-7 was optimal. The minimum reflection loss (RLmin) of SiCN-7 reached -53.47 dB at 4.2 mm and the effective absorption bandwidth (EAB) was 2.32 GHz at 3.48 mm. Through the analysis of electrical conductivity, it was found that the proportion of polarization loss in dielectric loss was more than 99%. It is worth noting that the radar cross section (RCS) value of SiCN-7 absorber was lower than that of the perfect electrical conductor (PEC) plate in the range of -90-90°, and showed a larger coverage angle, indicating that it possessed a good practical application prospect in the field of electromagnetic wave absorption.

Isolation, identification, and proteomic analysis of outer membrane vesicles of Riemerella anatipestifer SX-1.

Riemerella anatipestifer, belonging to Weeksellaceae family Riemerella, is a bacterium that can infect ducks, geese, and turkeys, causing diseases known as duck infectious serositis, new duck disease, and duck septicemia. We collected diseased materials from ducks on a duck farm in China and then isolated and purified a strain of serotype 1 R. anatipestifer named SX-1. Animal experiments showed that SX-1 is a highly virulent strain with an LD50 value of 101 CFU/mL. The complete genome sequence was obtained. The complete genome sequence of R. anatipestifer SX-1 was 2,112,539 bp; 847 genes were involved in catalytic activity, and 445 genes were related to the cell membrane. The total length of the repetitive sequences was 8746 bp. Four CRISPR loci were predicted in R. anatipestifer strain SX-1, and 4 genomic islands were predicted. Concentration and ultra-high-speed centrifugation were used to extract the outer membrane vesicles of R. anatipestifer SX-1. The OMVs were extracted successfully. Particle size analysis revealed the size and abundance of particles: 147.4 nm, 94.9%; 293.6 nm, 1.1%; 327.2 nm, 1.1%; 397.2 nm, 0.3%; and 371.8 nm, 1.1%. The average size was 173.5 nm. Label-free proteomic technology was used to identify proteins in the outer membrane vesicles. ATCC 11845 served as the reference genome sequence, and 148 proteins were identified using proteomic analysis, which were classified into 5 categories based on their sources. Among them, 24 originated from cytoplasmic proteins, 4 from extracellular secreted proteins, 27 from outer membrane proteins, 10 from periplasmic proteins, and 83 from unknown sources. This study conducted a proteomic analysis of OMVs to provide a theoretical basis for the development of R. anatipestifer OMVs vaccines and adjuvants and lays the foundation for further research on the relationship between the pathogenicity of R. anatipestifer and OMVs.

Characterization of a novel recombinant NADC30­like porcine reproductive and respiratory syndrome virus in Shanxi Province, China.

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important pathogens affecting the swine industry. In this report, a novel PRRSV strain SXht2012 was isolated from Shanxi province in China. To identify genetic characteristics of SXht2012, we conducted phylogenetic and homology analyses after sequencing its complete genome. The results revealed that SXht2012 belonged to NADC30-like strain and shared 91.3% nucleotide (nt) identity with strain NADC30. Notably, sequence alignment showed that a distinctive feature in the NSP2 region, where a 131-amino acid (aa) deletion was found in the hypervariable region (HVR). Additionally, variations were also detected in the GP5 protein, specifically in the decoy peptide, T cell peptide, and a potential glycosylation site (aa 32). Furthermore, we also found that SXht2012 was likely a recombination virus originating from NADC30-like and JXA1-like strains, and three recombination breakpoints were identified in the genome at nt positions 1516, 5280 and 6851, which correspond to the NSP2, NSP3, and NSP7 regions. Overall, these findings have significant implications for understanding the genetic variation and evolutionary dynamics of PRRSV strains.

DEAD-box helicase 1 inhibited CD8+ T cell antitumor activity by inducing PD-L1 expression in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) does not respond well to current treatments, even immune checkpoint inhibitors. PD-L1 (programmed cell death ligand 1 or CD274 molecule)-mediated immune escape of tumor cells may be a key factor affecting the efficacy of immune checkpoint inhibitor (ICI) therapy. However, the regulatory mechanisms of PD-L1 expression and immune escape require further exploration. Here, we observed that DDX1 (DEAD-box helicase 1) was overexpressed in HCC tissues and associated with poor prognosis in patients with HCC. Additionally, DDX1 expression correlated negatively with CD8+ T cell frequency. DDX1 overexpression significantly increased interferon gamma (IFN-γ)-mediated PD-L1 expression in HCC cell lines. DDX1 overexpression decreased IFN-γ and granzyme B production in CD8+ T cells and inhibited CD8+ T cell cytotoxic function in vitro and in vivo. In conclusion, DDX1 plays an essential role in developing the immune escape microenvironment, rendering it a potential predictor of ICI therapy efficacy in HCC.

Low 18F-fluorodeoxyglucose dose positron emission tomography assisted by a deep-learning image-denoising technique in patients with lymphoma.

Background: Patients with lymphoma receive multiple positron emission tomography/computed tomography (PET/CT) exams for monitoring of the therapeutic response. With PET imaging, a reduced level of injected fluorine-18 fluorodeoxyglucose ([18F]FDG) activity can be administered while maintaining the image quality. In this study, we investigated the efficacy of applying a deep learning (DL) denoising-technique on image quality and the quantification of metabolic parameters and Deauville score (DS) of a low [18F]FDG dose PET in patients with lymphoma. Methods: This study retrospectively enrolled 62 patients who underwent [18F]FDG PET scans. The low-dose (LD) data were simulated by taking a 50% duration of routine-dose (RD) PET list-mode data in the reconstruction, and a U-Net-based denoising neural network was applied to improve the images of LD PET. The visual image quality score (1 = undiagnostic, 5 = excellent) and DS were assessed in all patients by nuclear radiologists. The maximum, mean, and standard deviation (SD) of the standardized uptake value (SUV) in the liver and mediastinum were measured. In addition, lesions in some patients were segmented using a fixed threshold of 2.5, and their SUV, metabolic tumor volume (MTV), and tumor lesion glycolysis (TLG) were measured. The correlation coefficient and limits of agreement between the RD and LD group were analyzed. Results: The visual image quality of the LD group was improved compared with the RD group. The DS was similar between the RD and LD group, and the negative (DS 1-3) and positive (DS 4-5) results remained unchanged. The correlation coefficients of SUV in the liver, mediastinum, and lesions were all >0.85. The mean differences of SUVmax and SUVmean between the RD and LD groups, respectively, were 0.22 [95% confidence interval (CI): -0.19 to 0.64] and 0.02 (95% CI: -0.17 to 0.20) in the liver, 0.13 (95% CI: -0.17 to 0.42) and 0.02 (95% CI: -0.12 to 0.16) in the mediastinum, and -0.75 (95% CI: -3.42 to 1.91), and -0.13 (95% CI: -0.57 to 0.31) in lesions. The mean differences in MTV and TLG were 0.85 (95% CI: -2.27 to 3.98) and 4.06 (95% CI: -20.53 to 28.64) between the RD and LD groups. Conclusions: The DL denoising technique enables accurate tumor assessment and quantification with LD [18F]FDG PET imaging in patients with lymphoma.

Solitary bone plasmacytoma of spine with involvement of intervertebral disk: a case report and literature review.

Primary malignant bone tumors of the spine are exceedingly rare, with solitary bone plasmacytoma (SBP) representing approximately 30% of all cases. Radiological assessments are crucial for localizing SBP and for ruling out a diagnosis of multiple myeloma (MM). Imaging features resembling a "mini-brain" appear to be distinctive for SBP. Vertebral lesions accompanied by adjacent disc space involvement typically suggest spinal infections, while the potential for SBP involvement is often overlooked. We present a case of a 61-year-old female with SBP who exhibited thoraco-lumbar spine destruction and adjacent disc space involvement. The patient sought treatment at our medical center due to lumbodorsal pain radiating bilaterally to the inguinal regions. Radiological findings revealed an osteolytic lesion involving the intervertebral disc, making it challenging to distinguish between tumor and inflammation. A biopsy of the vertebral lesion confirmed the diagnosis of SBP, which was further supported by laboratory results. Post-diagnosis, the patient underwent radiotherapy, receiving a total dose of 4000 Gy, which alleviated her symptoms. We also provide a comprehensive literature review on SBP with disc involvement to aid both clinical and radiological diagnoses.

Discovery and Optimization of WDR5 Inhibitors via Cascade Deoxyribonucleic Acid-Encoded Library Selection Approach.

The DNA-encoded library (DEL) is a powerful hit generation tool for chemical biology and drug discovery; however, the optimization of DEL hits remained a daunting challenge for the medicinal chemistry community. In this study, hit compounds targeting the WIN binding domain of WDR5 were discovered by the initial three-cycle linear DEL selection, and their potency was further enhanced by a cascade DEL selection from the focused DEL designed based on the original first run DEL hits. As expected, these new compounds from the second run of focused DEL were more potent WDR5 inhibitors in the protein binding assay confirmed by the off-DNA synthesis. Interestingly, selected inhibitors exhibited good antiproliferative activity in two human acute leukemia cell lines. Taken together, this new cascade DEL selection strategy may have tremendous potential for finding high-affinity leads against WDR5 and provide opportunities to explore and optimize inhibitors for other targets.

High-throughput computational materials screening of transition metal peroxides.

Semiconductor materials of abnormal stoichiometric ratio often exhibit unique properties, yet it is still a challenge to determine the structures of such materials in an efficient way. Herein, we propose a method for structurally biased screening according to the coordination numbers and the numbers of Wyckoff positions, balancing the atom local environment and the global symmetry of structures. Based on first-principles calculations, we have predicted two metastable peroxides P21/c-ScO2 and Pmmn-TiO3 with more than six coordination points. For these two structures, the most stable intrinsic defect is the oxygen vacancy (VO) at the peroxide anion (O2-2), which induces the absence of antibonding orbital formed by O2-2 near the valence band maximum. With the introduction of VO, the decrease of coordination numbers leads to charge recombination, and results in the appearance of an ordered phase TiO2.5 with stronger Ti-O orbital hybridization. The proposed method presents a promising and feasible approach for the screening of novel compounds.

Discovery of JN122, a Spiroindoline-Containing Molecule that Inhibits MDM2/p53 Protein-Protein Interaction and Exerts Robust In Vivo Antitumor Efficacy.

MDM2 and MDM4 cooperatively and negatively regulate p53, while this pathway is often hijacked by cancer cells in favor of their survival. Blocking MDM2/p53 interaction with small-molecule inhibitors liberates p53 from MDM2 mediated degradation, which is an attractive strategy for drug discovery. We reported herein structure-based discovery of highly potent spiroindoline-containing MDM2 inhibitor (-)60 (JN122), which also exhibited moderate activities against MDM4/p53 interactions. In a panel of cancer cell lines harboring wild type p53, (-)60 efficiently promoted activation of p53 and its target genes, inhibited cell cycle progression, and induced cell apoptosis. Interestingly, (-)60 also promoted degradation of MDM4. More importantly, (-)60 exhibited good PK properties and exerted robust antitumor efficacies in a systemic mouse xenograft model of MOLM-13. Taken together, our study showcases a class of potent MDM2 inhibitors featuring a novel spiro-indoline scaffold, which is promising for future development targeting cancer cells with wild-type p53.

Estimation of the random incidence sound absorption coefficients of different size rectangular samples.

The sound absorption coefficient (SAC) of materials measured in a reverberation room is affected by both the intrinsic properties of the material and geometrical dimensions of the sample. A different size of the same material may produce a different SAC primarily due to the edge effect phenomenon. In this research, the experimental data from multiple laboratories was analyzed to evaluate the influence of the edge effect. An empirical function was established based on these measurement data and the linear relationship between the SAC and the relative edge length. Thomasson's method, the two geometric methods, and the analytical method were used to estimate the SAC of an absorber from measurements on a different size sample and compared with results obtained using the empirical function. The results show that the proposed empirical method is a reliable way to predict the SAC of a sample from measurements on a different size sample of the same material, which only requires the thickness, density, and size of the material.

Generalized Octet Rule with Fractional Occupancies for Boron.

The octet rule is a fundamental theory in the chemical bonding of main-group elements, which achieve stable configurations by gaining, losing, or sharing electrons. However, the conventional octet rule, as depicted through Lewis structures, is inadequate for describing the electron delocalization in boron allotropes and boron-rich compounds due to the electron deficiency of boron. To address this, we introduce the concept of fractional electron occupancies, which more accurately reflect the electron delocalization in boron systems. Based on this, we propose a generalized octet rule that provides a more comprehensive understanding of the complex bonding configurations in boron allotropes and boron-rich compounds. Importantly, our predictions for α-B12 are validated by both first-principles calculations and existing experimental data. Beyond boron, this generalized octet rule is also applicable to systems with multiple resonance structures.

Room-Temperature Magnetic Phase Transition in an Electrically Tuned van der Waals Ferromagnet.

Finding tunable van der Waals (vdW) ferromagnets that operate at above room temperature is an important research focus in physics and materials science. Most vdW magnets are only intrinsically magnetic far below room temperature and magnetism with square-shaped hysteresis at room temperature has yet to be observed. Here, we report magnetism in a quasi-2D magnet Cr_{1.2}Te_{2} observed at room temperature (290 K). This magnetism was tuned via a protonic gate with an electron doping concentration up to 3.8×10^{21} cm^{-3}. We observed nonmonotonic evolutions in both coercivity and anomalous Hall resistivity. Under increased electron doping, the coercivities and anomalous Hall effects (AHEs) vanished, indicating a doping-induced magnetic phase transition. This occurred up to room temperature. DFT calculations showed the formation of an antiferromagnetic (AFM) phase caused by the intercalation of protons which induced significant electron doping in the Cr_{1.2}Te_{2}. The tunability of the magnetic properties and phase in room temperature magnetic vdW Cr_{1.2}Te_{2} is a significant step towards practical spintronic devices.

Highly enhanced hydrazine oxidation on bifunctional Ni tailored by alloying for energy-efficient hydrogen production.

The low-potential hydrazine oxidation reaction (HzOR) can replace the oxygen evolution reaction (OER) and thus assemble with the hydrogen evolution reaction (HER), consequently achieving energy-saving hydrogen (H2) production. Notably, developing sophisticated bifunctional electrocatalysts for HER and HzOR is a prerequisite for efficient H2 production. Alloying noble metals with eligible non-precious ones can increase affordability, catalytic activity, and stability, alongside rendering bifunctionality. Herein, RuNi alloy deposited onto carbon (RuNi/C) was directly prepared by a simple and highly practical co-reduction method, showing excellent performance for HER and HzOR. Interestingly, to achieve 10 mA cm-2, RuNi/C only required an ultralow potential of 24 mV for HER, on par with commercial 20 wt% platinum in carbon (Pt/C), and -65 mV for HzOR, surpassing most reported counterparts. Moreover, the two-electrode electrolyzer only required small operation voltages of 57.8 and 327 mV to drive 10 and 100 mA cm-2, respectively. Driven by a homemade hydrazine (N2H4) fuel cell and solar panel, appreciable H2 yields of 1.027 and 1.406 mmol h-1 were achieved, respectively, exhibiting the energy-saving advantages alongside robust practicability. Moreover, theoretical calculations revealed that alloying with Ru endows bifunctional Ni sites not only with a lower H2O dissociation barrier but also with more favorable H* adsorption alongside the reduced energy barrier between HzOR intermediates.

High Concentration Intrinsic Defects in MnSb2Te4.

MnSb2Te4 has a similar structure to an emerging material, MnBi2Te4. According to earlier theoretical studies, the formation energy of Mn antisite defects in MnSb2Te4 is negative, suggesting its inherent instability. This is clearly in contrast to the successful synthesis of experimental samples of MnSb2Te4. Here, the growth environment of MnSb2Te4 and the intrinsic defects are correspondingly investigated. We find that the Mn antisite defect is the most stable defect in the system, and a Mn-rich growth environment favors its formation. The thermodynamic equilibrium concentrations of the Mn antisite defects could be as high as 15% under Mn-poor conditions and 31% under Mn-rich conditions. It is also found that Mn antisite defects prefer a uniform distribution. In addition, the Mn antisite defects can modulate the interlayer magnetic coupling in MnSb2Te4, leading to a transition from the ideal antiferromagnetic ground state to a ferromagnetic state. The ferromagnetic coupling effect can be further enhanced by controlling the defect concentration.

Design, Construction, and Screening of Diversified Pyrimidine-Focused DNA-Encoded Libraries.

Pyrimidine is a ubiquitous component in natural products and approved drugs, providing an ideal modular scaffold for generating libraries with drug-like properties. DNA-encoded library technology introduces a novel library modality where each small molecule is covalently linked to a unique oligo tag. This technology offers the advantages of rapidly generating and interrogating large-scale libraries containing billions of members, substantially reducing the entry barrier to their use in both academia and the pharmaceutical industry. In this Letter, we describe the synthesis of three DNA-encoded libraries based on different functionalized pyrimidine cores featuring diversified chemoselectivity and regioselectivity. Preliminary screening of these DNA-encoded libraries against BRD4 identified compounds with nanomolar inhibition activities.

Associations between adiposity, diabetes, lifestyle factors and the risk of gliomas.

Background: Despite numerous observational studies linking adiposity, diabetes, and lifestyle factors with gliomas, the causal associations between them remain uncertain. Methods: This study aimed to use two-sample Mendelian randomization (MR) analysis to investigate whether these associations are causal. Specifically, independent genetic variants in body mass index (BMI), waist circumference (WC), type 2 diabetes (T2D), smoking, alcohol, and coffee consumption were extracted from the published genome-wide association studies (GWASs) with genome-wide significance. The corresponding summary-level data for gliomas were available from a GWAS of 1,856 cases and 4,955 controls of European descent from the GliomaScan consortium. Additionally, glioma pathogenesis-related protein 1 data were used for validation, and Radial MR analysis was conducted to examine the potential outlier single-nucleotide polymorphisms (SNPs). Results: One standard deviation (SD) increase in BMI had an odds ratio (OR) of 1.392 (95% confidence interval (CI), 0.935-2.071) for gliomas, while one SD increase in WC had an OR of 0.967 (95% CI, 0.547-1.710). For T2D, a one-unit increase in log-transformed OR had an OR of 0.923 (95% CI, 0.754-1.129). The prevalence of smoking initiation had an OR of 1.703 (95% CI, 0.871-3.326) for gliomas, while the prevalence of alcohol intake frequency had an OR of 0.806 (95% CI, 0.361-1.083), and the prevalence of coffee intake had an OR of 0.268 (95% CI, 0.033-2.140) for gliomas. Conclusion: This study provides evidence that adiposity, T2D, smoking, alcohol drinking, and coffee intake do not play causal roles in the development of gliomas. The findings highlight the importance of reconsidering causal relationships in epidemiological research to better understand the risk factors and prevention strategies for gliomas.

Genomic Characterization and gE/gI-Deleted Strain Construction of Novel PRV Variants Isolated in Central China.

Pseudorabies virus (PRV) variants have caused substantial economic losses in the swine industry in China since 2011. To surveil the genetic variation in PRV field strains, here, two novel variant strains of PRV were isolated from Shanxi Province in central China and were designated SX1910 and SX1911. To identify the genetic characteristics of the two isolates, their complete genomes were sequenced, and phylogenetic analysis and sequence alignment revealed that field PRV variants have undergone genetic variations; notably, the protein-coding sequences UL5, UL36, US1 and IE180 exhibited extensive variation and contained one or more hypervariable regions. Furthermore, we also found that the glycoproteins gB and gD of the two isolates had some novel amino acid (aa) mutations. Importantly, most of these mutations were located on the surface of the protein molecule, according to protein structure model analysis. We constructed a mutant virus of SX1911 with deletion of the gE and gI genes via CRISPR/Cas9. When tested in mice, SX1911-ΔgE/gI-vaccinated mice were protected within a comparable range to Bartha-K61-vaccinated mice. Additionally, a higher dose of inactivated Bartha-K61 protected the mice from lethal SX1911 challenge, while a lower neutralization titer, higher viral load and more severe microscopic lesions were displayed in Bartha-K61-vaccinated mice. These findings highlight the need for continuous monitoring of PRV and novel vaccine development or vaccination program design for PRV control in China.