Detection and characterization of spontaneous internal deletion mutants of Beet Necrotic yellow vein virus RNA3 from systemic host Nicotiana benthamiana

Abstract Background Beet Necrotic Yellow Vein virus (BNYVV) is a member of the genus Benyvirus causing a worldwide sugar beet disease rhizomania. BNYVV contains four or five plus-sense single stranded RNAs. In altered selective conditions, multipartite RNA viruses of plant are prone to undergoing internal deletions, thus turning into Defective RNAs (D RNAs). Although several D RNAs have been reported in BNYVV infection, the spontaneous internal deletion mutants responsible for severe symptom in systemic host Nicotiana benthamiana (N. benthamiana) are not described so far. Results Systemic host N. benthamiana was inoculated by Chinese BNYVV isolates. RT-PCR and Northern blot showed that the D RNAs forms of BNYVV RNA3 were present in the systemic infection of the N. benthamiana. Three distinct D-RNA3s, named as D-RNA 3α, D-RNA 3β and D-RNA 3γ, were made into infectious clones. When inoculated on the N. benthamiana, the in vitro transcripts of D forms exhibited more stable than that of wild-type RNA3 in systemic movement. Among the detected mutant, the p25 protein frame-shift mutant (D-RNA3α) induced obvious necrotic lesions on Tetragonia.expansa (T. expansa) and pronounced systemic symptom on the N. benthamiana. The D-RNA3α was further mutated artificially to pre-terminate the downstream N protein, leading to the abolishment of the pathogenicity, indicating the N protein was responsible for the necrotic symptom. Conclusion Our studies demonstrated the internal deletion mutants of BNYVV-RNA3 were spontaneously generated in the systemic infection on N. benthamiana. The internal deletions didn't affect the efficient replication of D-RNA3s, instead by improving the stability and pathogenicity of RNA3 in the systemic host N. benthamiana. Besides, our results also suggested the downstream N protein of RNA3, but not the upstream p25 protein, may play an important role in the systemic infection on N. benthamiana

Efferocytosis signatures as prognostic markers for revealing immune landscape and predicting immunotherapy response in hepatocellular carcinoma

Background: Hepatocellular carcinoma (HCC) is a highly lethal liver cancer with late diagnosis; therefore, the identification of new early biomarkers could help reduce mortality. Efferocytosis, a process in which one cell engulfs another cell, including macrophages, dendritic cells, NK cells, etc., plays a complex role in tumorigenesis, sometimes promoting and sometimes inhibiting tumor development. However, the role of efferocytosis-related genes (ERGs) in HCC progression has been poorly studied, and their regulatory effects in HCC immunotherapy and drug targeting have not been reported.Methods: We downloaded efferocytosis-related genes from the Genecards database and screened for ERGs that showed significant expression changes between HCC and normal tissues and were associated with HCC prognosis. Machine learning algorithms were used to study prognostic gene features. CIBERSORT and pRRophetic R packages were used to evaluate the immune environment of HCC subtypes and predict treatment response. CCK-8 experiments conducted on HCC cells were used to assess the reliability of drug sensitivity prediction.Results: We constructed a prognostic prediction model composed of six genes, and the ROC curve showed good predictive accuracy of the risk model. In addition, two ERG-related subgroups in HCC showed significant differences in tumor immune landscape, immune response, and prognostic stratification. The CCK-8 experiment conducted on HCC cells confirmed the reliability of drug sensitivity prediction.Conclusion: Our study emphasizes the importance of efferocytosis in HCC progression. The risk model based on efferocytosis-related genes developed in our study provides a novel precision medicine approach for HCC patients, allowing clinicians to customize treatment plans based on unique patient characteristics. The results of our investigation carry noteworthy implications for the development of individualized treatment approaches involving immunotherapy and chemotherapy, thereby potentially facilitating the realization of personalized and more efficacious therapeutic interventions for HCC

9-(1,1-Dimethyl-3-oxobut­yl)adenine

The title compound, C11H15N5O, crystallizes with two independent mol­ecules in the asymmetric unit, both of which contain essentially planar imidazole and pyrimidine rings [maximum deviations = 0.002 (2) and 0.026 (2) Å, respectively, for the first mol­ecule, and 0.001 (2) and 0.025 (2) Å for the second]; the dihedral angles between the rings are 2.1 (2) and 1.7 (2)° in the two mol­ecules. The crystal structure is stabilized by inter­molecular N—H⋯N hydrogen bonds, defining chains along a, which are further linked by weak inter­molecular π–π contacts [centroid centroid distance = 3.7989 (16) Å] into planes parallel to (01)

27-Hydroxycholesterol Contributes to Lysosomal Membrane Permeabilization-Mediated Pyroptosis in Co-cultured SH-SY5Y Cells and C6 Cells

Purpose: Emerging evidence suggests that 27-Hydroxycholesterol (27-OHC) causes neurodegenerative diseases through the induction of cytotoxicity and cholesterol metabolism disorder. The objective of this study is to determine the impacts of 27-OHC on lysosomal membrane permeabilization (LMP) and pyroptosis in neurons in the development of neural degenerative diseases.Methods: In this study, SH-SY5Y cells and C6 cells were co-cultured in vitro to investigate the influence of 27-OHC on the function of lysosome, LMP and pyroptosis related factors in neuron. Lyso Tracker Red (LTR) was used to detect the changes of lysosome pH, volume and number. Acridine orange (AO) staining was also used to detect the LMP in neurons. Then the morphological changes of cells were observed by a scanning electron microscope (SEM). The content of lysosome function associated proteins [including Cathepsin B (CTSB), Cathepsin D (CTSD), lysosomal-associated membraneprotein-1 (LAMP-1), LAMP-2] and the pyroptosis associated proteins [including nod-like recepto P3 (NLRP3), gasdermin D (GSDMD), caspase-1 and interleukin (IL)-1β] were detected through Western blot.Results: Results showed higher levels of lysosome function associated proteins, such as CTSB (p < 0.05), CTSD (p < 0.05), LAMP-1 (p < 0.01), LAMP-2; p < 0.01) in 27-OHC treated group than that in the control group. AO staining and LTR staining showed that 27-OHC induced lysosome dysfunction with LMP. Content of pyroptosis related factor proteins, such as GSDMD (p < 0.01), NLRP3 (p < 0.001), caspase-1 (p < 0.01) and IL-1β (p < 0.01) were increased in 27-OHC treated neurons. Additionally, CTSB was leaked through LMP into the cytosol and induced pyroptosis. Results from the present study also suggested that the CTSB is involved in activation of pyroptosis.Conclusion: Our data indicate that 27-OHC contributes to the pathogenesis of cell death by inducing LMP and pyroptosis in neurons

Association of cluster determinant 36, scavenger receptor class B type 1, and major facilitator superfamily domain containing the 2a genetic polymorphism with serum lipid profile in aging population with type 2 diabetes mellitus

Background Lipid metabolism disorder commonly happens in subjects with Type 2 diabetes mellitus (T2DM) which may be linked to genetic variants of lipid metabolism-related genes. However, few studies have explored the relationship between lipid metabolism-related gene polymorphism and serum lipid profile in aging subjects with T2DM. The present study was designed to explore the impact of genetic polymorphism of cluster determinant 36 (CD36) (rs1049673, rs1054516, rs2151916), scavenger receptor class B type 1 (SCARB1) (rs5888), and major facilitator superfamily domain containing the 2a (MFSD2A) (rs12083239, rs4233508, rs12072037) on the relationship between circulating lipids in aging subjects with T2DM. Methods 205 T2DM patients and 205 age and gender matched control subjects were recruited. Information on demographic characteristics was collected by using a self-administered questionnaire. Fasting venous blood samples were taken for lipid-related gene genotyping and serum lipid profile measurement. The Chi-square test was used to compare percentage differences and to calculate P-value for Hardy-Weinberg equilibrium. Logistic regression and multiple linear regression were used to explore the risk or correlation between variables, and general linear model (GLM) was used to compare the means of serum lipids between the groups. Results In T2DM group, CD36 rs1054516 and MFSD2A rs12072037 were correlated with serum TC level. In control group, CD36 rs1049673 was correlated with serum HDL-C level. Meanwhile, T2DM subjects with MFSD2A rs12083239 (CG), MFSD2A rs4233508 (TT), and MFSD2A rs12072037 (AA) had higher TG level than control subjects. T2DM subjects with CD36 rs1049673 (CG, GG), CD36 rs1054516 (CT), CD36 rs2151916 (TT, CT), SCARB1 rs5888 (GG), MFSD2A rs12083239 (GG, CG), MFSD2A rs4233508 (TT), and MFSD2A rs12072037 (CA, AA) had lower HDL-C level than control subjects. T2DM subjects with MFSD2A rs12072037 (AA) had lower LDL-C level than control subjects. In dominant model, major genotype (GG) of SCARB1 gene was associated with the risk of T2DM (OR = 0.636, P = 0.032). Conclusion The genetic polymorphism of CD36 (rs1049673, rs1054516, rs2151916), SCARB1 (rs5888), and MFSD2A (rs12083239, rs4233508, rs12072037) were associated with serum lipids in T2DM subjects. The SCARB1 rs5888 major genotype (GG) was a protective factor for T2DM. Large scale cohort study is required to determine the relationship between lipid metabolism-related gene polymorphism, serum lipid profile and T2DM in aging subjects

Selective Ethylene Glycol Oxidation to Formate on Nickel Selenide with Simultaneous Evolution of Hydrogen

There is an urgent need for cost-effective strategies to produce hydrogen from renewable net-zero carbon sources using renewable energies. In this context, the electrochemical hydrogen evolution reaction can be boosted by replacing the oxygen evolution reaction with the oxidation of small organic molecules, such as ethylene glycol (EG). EG is a particularly interesting organic liquid with two hydroxyl groups that can be transformed into a variety of C1 and C2 chemicals, depending on the catalyst and reaction conditions. Here, a catalyst is demonstrated for the selective EG oxidation reaction (EGOR) to formate on nickel selenide. The catalyst nanoparticle (NP) morphology and crystallographic phase are tuned to maximize its performance. The optimized NiS electrocatalyst requires just 1.395 V to drive a current density of 50 mA cm −2 in 1 potassium hydroxide (KOH) and 1 EG. A combination of in situ electrochemical infrared absorption spectroscopy (IRAS) to monitor the electrocatalytic process and ex situ analysis of the electrolyte composition shows the main EGOR product is formate, with a Faradaic efficiency above 80%. Additionally, C2 chemicals such as glycolate and oxalate are detected and quantified as minor products. Density functional theory (DFT) calculations of the reaction process show the glycol-to-oxalate pathway to be favored via the glycolate formation, where the C-C bond is broken and further electro-oxidized to formate. A combination of in situ and ex situ analysis shows the main product of the ethylene glycol (EG) oxidation reaction (EGOR) is formate with a Faradaic efficiency above 80%, and glycolate and oxalate as minor chemicals on nickel selenide nanoparticles (NPs). Further density functional theory (DFT) calculation reveals the electrooxidation mechanism to these products

Novel Fe-Mn-Si-Pd alloys: insights on mechanical, magnetic, corrosion performance and biocompatibility

Two new Fe-based alloys, Fe-10Mn6Si1Pd and Fe-30Mn6Si1Pd, have been fabricated by arc-melting followed by copper mold suction casting. The Fe-30Mn6Si1Pd alloy mainly consists of ε-martensite and γ-austenite Fe-rich phases whereas the Fe-10Mn6Si1Pd alloy primarily contains α-Fe(Mn)-ferrite phase. Additionally, Pd-rich precipitates were detected in both alloys. Good mechanical response was observed by nanoindentation: hardness values around 5.6 GPa and 4.2 GPa and reduced Young's modulus values of 125 GPa and 93 GPa were measured for the as-prepared Fe-10Mn6Si1Pd and Fe-30Mn6Si1Pd alloys, respectively. Both alloys are thus harder and exhibit lower Young's modulus than 316L stainless steel, which is one of the most common Fe-based reference materials for biomedical applications. Compared with the ferromagnetic Fe-10Mn6Si1Pd alloy, the paramagnetic Fe-30Mn6Si1Pd alloy is more appropriate to be used as an implant since it would be compatible with nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) analyses. Concerning biocompatibitliy, the more hydrophilic Fe-10Mn6Si1Pd shows improved cell adhesion but its pronounced ion leaching has a negative effect on the proliferation of cells. The influence of immersion in simulated body fluid on composition, microstructure, mechanical and magnetic properties of both alloys is assessed, and the correlation between microstructure evolution and physical properties is discussed

Electrochemical reforming of ethanol with acetate Co-Production on nickel cobalt selenide nanoparticles

The energy efficiency of water electrolysis is limited by the sluggish reaction kinetics of the anodic oxygen evolution reaction (OER). To overcome this limitation, OER can be replaced by a less demanding oxidation reaction, which in the ideal scenario could be even used to generate additional valuable chemicals. Herein, we focus on the electrochemical reforming of ethanol in alkaline media to generate hydrogen at a Pt cathode and acetate as a co-product at a NiCoSe anode. We first detail the solution synthesis of a series of NiCoSe electrocatalysts. By adjusting the Ni/Co ratio, the electrocatalytic activity and selectivity for the production of acetate from ethanol are optimized. Best performances are obtained at low substitutions of Ni by Co in the cubic NiSe phase. Density function theory reveals that the Co substitution can effectively enhance the ethanol adsorption and decrease the energy barrier for its first step dehydrogenation during its conversion to acetate. However, we experimentally observe that too large amounts of Co decrease the ethanol-to-acetate Faradaic efficiency from values above 90% to just 50 %. At the optimized composition, the NiCoSe electrode delivers a stable chronoamperometry current density of up to 45 mA cm, corresponding to 1.2 A g, in a 1 M KOH + 1 M ethanol solution, with a high ethanol-to-acetate Faradaic efficiency of 82.2% at a relatively low potential, 1.50 V vs. RHE, and with an acetate production rate of 0.34 mmol cm h.This work was supported by the start-up funding at Chengdu University. It was also supported by the European Regional Development Funds and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP (ENE2016-77798-C4-3-R), MCIN/ AEI/10.13039/501100011033/ project, and NANOGEN (PID2020-116093RB-C43). X. Wang, C. Xing, X. Han, R. He, Z. Liang, and Y. Zhang are grateful for the scholarship from China Scholarship Council (CSC). X. Han and J. Arbiol acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 acknowledges support from the Severo Ochoa Programme (MINECO, Grant no. SEV-2013-0295). IREC and ICN2 are funded by the CERCA Programme / Generalitat de Catalunya

Mutations in Polymerase Genes Enhanced the Virulence of 2009 Pandemic H1N1 Influenza Virus in Mice

Influenza A virus can infect a wide variety of animal species with illness ranging from mild to severe, and is a continual cause for concern. Genetic mutations that occur either naturally or during viral adaptation in a poorly susceptible host are key mechanisms underlying the evolution and virulence of influenza A virus. Here, the variants containing PA-A36T or PB2-H357N observed in the mouse-adapted descendants of 2009 pandemic H1N1 virus (pH1N1), A/Sichuan/1/2009 (SC), were characterized. Both mutations enhanced polymerase activity in mammalian cells. These effects were confirmed using recombinant SC virus containing polymerase genes with wild type (WT) or mutant PA or PB2. The PA-A36T mutant showed enhanced growth property compared to the WT in both human A549 cells and porcine PK15 cells in vitro, without significant effect on viral propagation in murine LA-4 cells and pathogenicity in mice; however, it did enhance the lung virus titer. PB2-H357N variant demonstrated growth ability comparable to the WT in A549 cells, but replicated well in PK15, LA-4 cells and in mice with an enhanced pathogenic phenotype. Despite such mutations are rare in nature, they could be observed in avian H5 and H7 subtype viruses which were currently recognized to pose potential threat to human. Our findings indicated that pH1N1 may adapt well in mammals when acquiring these mutations. Therefore, future molecular epidemiological surveillance should include scrutiny of both markers because of their potential impact on pathogenesis

Evaluation of unclassified variants in the breast cancer susceptibility genes BRCA1 and BRCA2 using five methods: results from a population-based study of young breast cancer patients

Introduction Efforts are ongoing to determine the significance of unclassified variants (UVs) in the breast cancer susceptibility genes BRCA1/BRCA2, but no study has systematically assessed whether women carrying the suspected deleterious UVs have characteristics commonly seen among women carrying known deleterious or disease-causing mutations in BRCA1/BRCA2. Methods We sequenced BRCA1/BRCA2 in 1,469 population-based female breast cancer patients diagnosed between the ages of 20 and 49 years. We used existing literature to classify variants into known deleterious mutations, polymorphic variants, and UVs. The UVs were further classified as high risk or low risk based on five methods: allele frequency, Polyphen algorithm, sequence conservation, Grantham matrix scores, and a combination of the Grantham matrix score and sequence conservation. Furthermore, we examined whether patients who carry the variants classified as high risk using these methods have risk characteristics similar to patients with known deleterious BRCA1/BRCA2 mutations (early age at diagnosis, family history of breast cancer or ovarian cancer, and negative estrogen receptor/progesterone receptor). Results We identified 262 distinct BRCA1/BRCA2 variants, including 147 UVs, in our study population. The BRCA1 UV carriers, but not the BRCA2 UV carriers, who were classified as high risk using each classification method were more similar to the deleterious mutation carriers with respect to family history than those carriers classified as low risk. For example, the odds ratio of having a first-degree family history for the high-risk women classified using Polyphen was 3.39 (95% confidence interval = 1.16 to 9.94) compared with normal/polymorphic BRCA1 carriers. The corresponding odds ratio of low-risk women was 1.53 (95% confidence interval = 1.07 to 2.18). The odds ratio for high-risk women defined by allele frequency was 2.00 (95% confidence interval = 1.14 to 3.51), and that of low-risk women was 1.30 (95% confidence interval = 0.87 to 1.93). Conclusion The results suggest that the five classification methods yielded similar results. Polyphen was particularly better at isolating BRCA1 UV carriers likely to have a family history of breast cancer or ovarian cancer, and may therefore help to classify BRCA1 UVs. Our study suggests that these methods may not be as successful in classifying BRCA2 UVs