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1.
Proc Natl Acad Sci U S A ; 120(3): e2217148120, 2023 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-36630453

RESUMO

Modulation of water activation is crucial to water-involved chemical reactions in heterogeneous catalysis. Organic sulfur (COS and CS2) hydrolysis is such a typical reaction involving water (H2O) molecule as a reactant. However, limited by the strong O-H bond in H2O, satisfactory CS2 hydrolysis performance is attained at high temperature above 310 °C, which is at the sacrifice of the Claus conversion, strongly hindering sulfur recovery efficiency improvement and pollution emissions control of the Claus process. Herein, we report a facile oxygen vacancy (VO) engineering on titanium-based perovskite to motivate H2O activation for enhanced COS and CS2 hydrolysis at lower temperature. Increased amount of VO contributed to improved degree of H2O dissociation to generate more active -OH, due to lower energy barrier for H2O dissociation over surface rich in VO, particularly VO clusters. Besides, low-coordinated Ti ions adjacent to VO were active sites for H2O activation. Consequently, complete conversion of COS and CS2 was achieved over SrTiO3 after H2 reduction treatment at 225 °C, a favorable temperature for the Claus conversion, at which both satisfying COS and CS2 hydrolysis performance and improved sulfur recovery efficiency can be obtained simultaneously. Additionally, the origin of enhanced hydrolysis activity from boosted H2O activation by VO was revealed via in-depth mechanism study. This provides more explicit direction for further design of efficacious catalysts for H2O-involved reactions.


Assuntos
Oxigênio , Titânio , Temperatura , Hidrólise , Água/química , Enxofre
2.
Mol Cell Proteomics ; 22(7): 100582, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37225018

RESUMO

Carbon metabolism is central to photosynthetic organisms and involves the coordinated operation and regulation of numerous proteins. In cyanobacteria, proteins involved in carbon metabolism are regulated by multiple regulators including the RNA polymerase sigma factor SigE, the histidine kinases Hik8, Hik31 and its plasmid-borne paralog Slr6041, and the response regulator Rre37. To understand the specificity and the cross-talk of such regulations, we simultaneously and quantitatively compared the proteomes of the gene knockout mutants for the regulators. A number of proteins showing differential expression in one or more mutants were identified, including four proteins that are unanimously upregulated or downregulated in all five mutants. These represent the important nodes of the intricate and elegant regulatory network for carbon metabolism. Moreover, serine phosphorylation of PII, a key signaling protein sensing and regulating in vivo carbon/nitrogen (C/N) homeostasis through reversible phosphorylation, is massively increased with a concomitant significant decrease in glycogen content only in the hik8-knockout mutant, which also displays impaired dark viability. An unphosphorylatable PII S49A substitution restored the glycogen content and rescued the dark viability of the mutant. Together, our study not only establishes the quantitative relationship between the targets and the corresponding regulators and elucidated their specificity and cross-talk but also unveils that Hik8 regulates glycogen accumulation through negative regulation of PII phosphorylation, providing the first line of evidence that links the two-component system with PII-mediated signal transduction and implicates them in the regulation of carbon metabolism.


Assuntos
Carbono , Synechocystis , Fosforilação , Carbono/metabolismo , Proteômica , Synechocystis/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Glicogênio/metabolismo , Nitrogênio , Regulação Bacteriana da Expressão Gênica
3.
Microb Pathog ; 186: 106503, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38142905

RESUMO

Porcine epidemic diarrhea (PED), caused by porcine epidemic diarrhea virus (PEDV), is an acute and highly contagious enteric disease with a high mortality rate in suckling piglets. Identification of proteins associated with PEDV infection may provide insights into the pathogenesis of this viral disease. In this study, we employed tandem mass tag (TMT) quantitative protein analysis to investigate proteomic changes in PK15 cells following PEDV infection, and differential protein expression profiles were obtained at 0 h, 24 h, and 48 h post-infection. Overall, a total of 6330 proteins were identified. Applying criteria for fold change >1.5 < 0.67 and p-values <0.05 resulted in the identification of 59 up-regulated proteins and 103 down-regulated proteins that exhibited significant alterations in the H24 group compared to the H0 group. The H48 group demonstrated significant upregulation of 110 proteins and downregulation of 144 proteins compared to the H0 group; additionally, there were also 10 upregulated and 30 downregulated proteins in the H48 group when compared to the H24 group. These differentially expressed proteins (DEPs) were involved in immune response regulation, signal transduction, lipid transport and metabolism processes as well as cell apoptosis pathways. Based on these DEPs, we propose that PEDV may disrupt signal transduction pathways along with lipid transport and metabolism processes leading to maximal viral replication, it may also trigger inflammatory cascades accordingly. These findings could provide valuable information for elucidating specific pathogenesis related to PEDV infection while contributing towards developing new antiviral strategies.


Assuntos
Vírus da Diarreia Epidêmica Suína , Doenças dos Suínos , Animais , Suínos , Vírus da Diarreia Epidêmica Suína/fisiologia , Proteômica/métodos , Proteínas/metabolismo , Transdução de Sinais , Lipídeos
4.
Environ Sci Technol ; 58(4): 2153-2161, 2024 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-38244211

RESUMO

Nitrous oxide (N2O) has a detrimental impact on the greenhouse effect, and its efficient catalytic decomposition at low temperatures remains challenging. Herein, the cobalt-based high-entropy oxide with a spinel-type structure (Co-HEO) is successfully fabricated via a facile coprecipitation method for N2O catalytic decomposition. The obtained Co-HEO catalyst displays more remarkable catalytic performance and higher thermal stability compared with single and binary Co-based oxides, as the temperature of 90% N2O decomposition (T90) is 356 °C. A series of characterization results reveal that the synergistic effect of multiple elements enhances the reducibility and augments oxygen vacancy in the high-entropy system, thus boosting the activity of the Co-HEO catalyst. Moreover, density functional theory (DFT) calculations and the temperature-programmed surface reaction (TPSR) with isotope labeling demonstrate that N2O decomposition on the Co-HEO catalyst follows the Langmuir-Hinshelwood (L-H) mechanism with the promotion of abundant oxygen vacancies. This work provides a fundamental understanding of the synergistic catalytic effect in N2O decomposition and paves the way for the novel environmental catalytic applications of HEO.


Assuntos
Cobalto , Óxidos , Entropia , Óxidos/química , Cobalto/química , Oxigênio
5.
Environ Sci Technol ; 58(9): 4428-4437, 2024 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-38400916

RESUMO

The adsorption and activation of pollutant molecules and oxygen play a critical role in the oxidation reaction of volatile organic compounds (VOCs). In this study, superior adsorption and activation ability was achieved by modulating the interaction between Pt nanoparticles (NPs) and UiO-66 (U6) through the spatial position effect. Pt@U6 exhibits excellent activity in toluene, acetone, propane, and aldehyde oxidation reactions. Spectroscopic studies, 16O2/18O2 kinetic isotopic experiments, and density functional theory (DFT) results jointly reveal that the encapsulated Pt NPs of Pt@U6 possess higher electron density and d-band center, which is conducive for the adsorption and dissociation of oxygen. The toluene oxidation reaction and DFT results indicate that Pt@U6 is more favorable to activate the C-H of toluene and the C═C of maleic anhydride, while Pt/U6 with lower electron density and d-band center exhibits a higher oxygen dissociation temperature and higher reactant activation energy barriers. This study provides a deep insight into the architecture-performance relation of Pt-based catalysts for the catalytic oxidation of VOCs.


Assuntos
Estruturas Metalorgânicas , Nanopartículas , Ácidos Ftálicos , Compostos Orgânicos Voláteis , Compostos Orgânicos Voláteis/química , Tolueno/química , Oxigênio
6.
Mol Cell Proteomics ; 21(12): 100440, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36356940

RESUMO

Ascorbate peroxidase (APEX)-based proximity labeling coupled with mass spectrometry has a great potential for spatiotemporal identification of proteins proximal to a protein complex of interest. Using this approach is feasible to define the proteome neighborhood of important protein complexes in a popular photosynthetic model cyanobacterium Synechocystis sp. PCC6803 (hereafter named as Synechocystis). To this end, we developed a robust workflow for APEX2-based proximity labeling in Synechocystis and used the workflow to identify proteins proximal to the photosystem II (PS II) oxygen evolution complex (OEC) through fusion APEX2 with a luminal OEC subunit, PsbO. In total, 38 integral membrane proteins (IMPs) and 93 luminal proteins were identified as proximal to the OEC. A significant portion of these proteins are involved in PS II assembly, maturation, and repair, while the majority of the rest were not previously implicated with PS II. The IMPs include subunits of PS II and cytochrome b6/f, but not of photosystem I (except for PsaL) and ATP synthases, suggesting that the latter two complexes are spatially separated from the OEC with a distance longer than the APEX2 labeling radius. Besides, the topologies of six IMPs were successfully predicted because their lumen-facing regions exclusively contain potential APEX2 labeling sites. The luminal proteins include 66 proteins with a predicted signal peptide and 57 proteins localized also in periplasm, providing important targets to study the regulation and selectivity of protein translocation. Together, we not only developed a robust workflow for the application of APEX2-based proximity labeling in Synechocystis and showcased the feasibility to define the neighborhood proteome of an important protein complex with a short radius but also discovered a set of the proteins that potentially interact with and regulate PS II structure and function.


Assuntos
Complexo de Proteína do Fotossistema II , Synechocystis , Complexo de Proteína do Fotossistema II/metabolismo , Proteoma/metabolismo , Oxigênio/metabolismo , Complexo de Proteína do Fotossistema I/metabolismo , Synechocystis/metabolismo
7.
J Proteome Res ; 22(4): 1255-1269, 2023 04 07.
Artigo em Inglês | MEDLINE | ID: mdl-36930737

RESUMO

Spatial proteome reorganization in response to a changing environment represents a different layer of adaptation mechanism in addition to differential expression of a subset of stress responsive genes in photosynthetic organisms. Profiling such reorganization events is critically important to extend our understanding how photosynthetic organisms adapt to adverse environments. Thus, we treated a unicellular photosynthetic model cyanobacterium, Synechocystis sp. PCC 6803 (hereafter referred to as Synechocystis), with five different types of abiotic stresses including nitrogen starvation, iron deficiency, cold, heat, and darkness, and systematically identified proteins showing stress-induced differential expression and/or redistribution between the membrane and the soluble fractions using a quantitative proteomics approach. A number of proteins showing such a redistribution in response to a single or multiple types of abiotic stresses were identified. These include 12 ribosomal proteins displaying unanimous cold-induced redistribution to the membrane and the protein FurA, a master regulator of iron acquisition, displaying iron deficiency- and nitrogen starvation-induced redistribution to the membrane. Such findings shed light on a novel regulatory mechanism underlying the corresponding stress responses, and establish the results in the present study as an important resource for future studies intended to understand how photosynthetic organisms cope with adverse environments.


Assuntos
Deficiências de Ferro , Synechocystis , Humanos , Proteoma/genética , Proteoma/metabolismo , Estresse Fisiológico , Synechocystis/genética , Synechocystis/metabolismo , Nitrogênio/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo
8.
Arch Virol ; 168(10): 256, 2023 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-37737963

RESUMO

Senecavirus A (SVA) can cause a vesicular disease in swine. It is a positive-strand RNA virus belonging to the genus Senecavirus in the family Picornaviridae. Positive-strand RNA viruses possess positive-sense, single-stranded genomes whose untranslated regions (UTRs) have been reported to contain cis-acting RNA elements. In the present study, a total of 100 SVA isolates were comparatively analyzed at the genome level. A highly conserved fragment (HCF) was found to be located in the 3D sequence and to be close to the 3' UTR. The HCF was computationally predicted to form a stem-loop structure. Eight synonymous mutations can individually disrupt the formation of a single base pair within the stem region. We found that SVA itself was able to tolerate each of these mutations alone, as evidenced by the ability to rescue all eight single-site mutants from their individual cDNA clones, and all of them were genetically stable during serial passaging. However, the replication-competent SVA could not be rescued from another cDNA clone containing all eight mutations. The failure to recover SVA might be attributed to disruption of the predicted stem-loop structure, whereas introduction of a wild-type HCF into the cDNA clone with eight mutations still had no effect on virus recovery. These results suggest that the putative stem-loop structure at the 3' end of the 3D sequence is a cis-acting RNA element that is required for SVA growth.


Assuntos
Picornaviridae , Animais , Suínos , DNA Complementar , Picornaviridae/genética , Vírus de RNA de Cadeia Positiva , Regiões 3' não Traduzidas/genética , Sequência Conservada
9.
Anal Chem ; 94(2): 748-757, 2022 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-34951537

RESUMO

Hydronephrosis is one of the most common diseases in urology. However, due to the difficulties in clinical trials and the lack of reliable in vitro platforms, the surgical indicators are not clear. Herein, the renal-on-chip with a force-sensitive resistor microfluidic platform was established to simulate the state of hydronephrosis. Cell counting kit-8 (CCK-8) and tight junction protein claudin-2 were detected on a renal-on-chip microfluidic platform with a force-sensitive resistor (ROC-FS). The results indicated that the ROC-FS had normal physiological functions and the cell viability on ROC-FS declined to around 40% after 48 h of hydronephrosis-simulated treatment. In addition, proteomics analysis of 15 clinical ureteropelvic junction obstruction (UPJO) samples showed that compared with normal children, a total of 50 common proteins were differentially expressed in UPJO children (P < 0.05, |log2fold change| ≥ 1). Metabolomic analysis of 39 clinical UPJO samples showed that a total of 241 metabolisms were dysregulated. Subsequent immunofluorescence and enzyme-linked immunosorbent assay (ELISA) analysis using ROC-FS were performed to identify the clinical multi-omics results for screening. All results pointed out that the TGF-ß-related signaling pathways and arginine-related metabolism signaling pathways were dysregulated and α-SMA, AGT, and AGA might be the potential biomarkers of hydronephrosis. In addition, correlation analysis of AGT and KLK1 with differential renal function (DRF) from clinical samples indicated good correlation coefficients (R2 0.923, 0.8742, 0.6412, and 0.8347). This demonstrates the state of hydronephrosis could be significantly correlated with the biomarkers. These findings could provide a reliable reference for determining surgical biomarkers clinically, and ROC could be further used in the analysis of other kidney diseases.


Assuntos
Hidronefrose , Nefropatias , Obstrução Ureteral , Humanos , Hidronefrose/diagnóstico , Hidronefrose/etiologia , Hidronefrose/cirurgia , Lactente , Rim/fisiologia , Microfluídica
10.
Microb Pathog ; 162: 105323, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-34843921

RESUMO

Pseudomonas aeruginosa strains are potential pathogens that cause respiratory diseases in minks, and caused serious economic loss to mink breeding industry. In this study, we identified antimicrobial resistance and virulence genes in 125 P. aeruginosa isolates from mink in China from 2011 to 2020. The results showed at least one mutation in the gyrA (Thr83Val or Asp87Gly) and parC (Ser87 Leu) genes as well as single mutations in 56 isolates. At least 4-fold reductions in the fluoroquinolone minimum inhibitory concentration values were found when tested in the presence of PAßN in 23 isolates, while 44 isolates were positive for the extended spectrum ß-lactamases and 15 antibiotic resistance genes were identified in this population with a prevalence between 1-32%, including qnrA, CTX-M-1G, ermB and C, cmlA, flor, catl, intl1, tetA, B, C, and D as well as sul1, 2, and 3 genes. Interestingly, one isolate carried ten resistance genes. Five virulence genes were detected, where exoS and algD were the most frequently detected (76.8%), which were followed by plcH (76%), lasB (73.6%), and pilB (31.2%). The isolates carrying the antibiotic resistance or virulence genes were genetically variable, suggesting a horizontal spread through the population. Hence, this study provides novel and important data on the resistance and pathogenicity of P. aeruginosa in farmed mink infections. These data provide important insights into the mechanism of fluoroquinolone resistance in P. aeruginosa, highlighting its usefulness in the treatment and control of P. aeruginosa infections in minks.


Assuntos
Infecções por Pseudomonas , Pseudomonas aeruginosa , Animais , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Farmacorresistência Bacteriana , Testes de Sensibilidade Microbiana , Vison , Infecções por Pseudomonas/tratamento farmacológico , Infecções por Pseudomonas/veterinária , Pseudomonas aeruginosa/genética , Virulência , Fatores de Virulência/genética
11.
Anal Chem ; 93(28): 9835-9844, 2021 07 20.
Artigo em Inglês | MEDLINE | ID: mdl-34232631

RESUMO

Insulin resistance (IR) is a typical sign of metabolic dysregulation caused by fine particulate matter (PM2.5), but the underlying signaling has not been clearly determined. Herein, a microfluidic liver-kidney microphysiological system (LK-MPS) is presented to assess the signaling pathways of IR generated by PM2.5 at 200 µg/mL for 24 h. The LK-MPS device consisted of a biomimetic liver-kidney architecture and reconstructed two circulation paths: the liver metabolism-kidney excretion (LM-KE) and kidney excretion-liver metabolism (KE-LM), by which PM2.5 is feasibly distributed in the two organs. Transmission electron microscopy (TEM) analysis revealed that PM2.5 can embed in the cytoplasm and nuclei, undergo transport by vesicles, and lead to the destruction of mitochondria. Further comprehensive immunofluorescence, enzyme-linked immunosorbent assays (ELISAs) and untargeted metabolomic analyses confirmed that PM2.5 disturbed the classic IRS-1/AKT signaling pathway (INSR, IRS-1, PI3K, AKT, GLUT2, GLUT4, and FOXO1 downregulated) and IR-related metabolic pathways: UDP-hexosamine (UDP-GlcNAc), gluconeogenesis (ß-d-glucose 6-phosphate), and lipid biosynthesis (ceramide (Cer) and triacylglycerol (TG)) pathways, leading to the disorder of glucose levels. Collectively, these disorders aggravate hepatic and renal IR. Pearson's correlation coefficient test showed that elemental carbon (EC), polycyclic aromatic hydrocarbons (PAHs), and metals (Ca, Co, and V) were negatively correlated to the dysregulated proteins (INSR, IRS-1, AKT, FOXO1, GLUT2, and GLUT4). These findings may partially explain IR-related signaling pathways triggered by PM2.5.


Assuntos
Resistência à Insulina , Insulina , Humanos , Rim/metabolismo , Fígado/metabolismo , Microfluídica , Material Particulado/toxicidade , Proteínas Proto-Oncogênicas c-akt/metabolismo , Transdução de Sinais
12.
J Am Soc Nephrol ; 31(10): 2263-2277, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32646856

RESUMO

BACKGROUND: Lipocalin-2 (LCN2) is an indicator of the severity of lupus nephritis (LN) and plays a pivotal role in immune responses, but it is not known if its effect on LN pathogenesis derives from regulating the immune imbalance of T lymphocyte subsets. METHODS: The expression of LCN2 in T cells and kidneys was assessed in renal biopsies from patients with LN. We investigated the relationship between LCN2 levels and development of LN and systemic illness by injecting anti-LCN2 antibodies into MRL/lpr mice and analyzing pristane-treated LCN2-/- mice. RESULTS: LCN2 is highly expressed in CD4+ T cells and in renal tissues, and is associated with severe renal damage in patients with LN and in mice with experimental lupus. LCN2 promotes IFN-γ overexpression in CD4+ T cells through the IL-12/STAT4 pathway in an autocrine or paracrine manner. Both neutralization of LCN2 in MRL/lpr mice and genetic depletion of LCN2 in pristane-induced lupus mice greatly ameliorate nephritis. The frequency and number of splenic and renal Th1 cells decrease in proportion to LN disease activity. Conversely, administration of LCN2 exacerbates the disease with significantly higher renal activity scores and increased numbers of Th1 cells. CONCLUSIONS: LCN2 plays a crucial role in Th1 cell differentiation, and may present a potential therapeutic target for LN.


Assuntos
Lipocalina-2/metabolismo , Nefrite Lúpica/metabolismo , Nefrite Lúpica/patologia , Células Th1/metabolismo , Animais , Estudos de Casos e Controles , Diferenciação Celular , Modelos Animais de Doenças , Feminino , Humanos , Nefrite Lúpica/etiologia , Masculino , Camundongos , Camundongos Endogâmicos MRL lpr , Células Th1/patologia
13.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 36(10): 1022-1024, 2019 Oct 10.
Artigo em Chinês | MEDLINE | ID: mdl-31598951

RESUMO

OBJECTIVE: To explore the genetic basis for a fetus suspected for congenital nephrotic syndrome of Finland (CNF). METHODS: Genomic DNA was extracted from peripheral and umbilical cord blood samples derived from both parents and the fetus. Potential variants were detected by using next-generation sequencing. Suspected variants were confirmed by Sanger sequencing. RESULTS: The fetus was found to carry compound heterozygous variants c.1440+1G>A and c.925G>T of the NPHS1 gene, which were respectively inherited from its mother and father. CONCLUSION: Identification of the compound heterozygous NPHS1 variants has enabled diagnosis of CNF in the fetus and genetic counseling for the affected family.


Assuntos
Síndrome Nefrótica/congênito , Síndrome Nefrótica/diagnóstico , Feminino , Feto , Finlândia , Heterozigoto , Humanos , Proteínas de Membrana/genética , Gravidez , Diagnóstico Pré-Natal
14.
J Proteome Res ; 17(5): 1812-1825, 2018 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-29611422

RESUMO

To gain a deep understanding of yeast-cell response to heat stress, multiple laboratory strains have been intensively studied via genome-wide expression analysis for the mechanistic dissection of classical heat-shock response (HSR). However, robust industrial strains of Saccharomyces cerevisiae have hardly been explored in global analysis for elucidation of the mechanism of thermotolerant response (TR) during fermentation. Herein, we employed data-independent acquisition and sequential window acquisition of all theoretical mass spectra based proteomic workflows to characterize proteome remodeling of an industrial strain, ScY01, responding to prolonged thermal stress or transient heat shock. By comparing the proteomic signatures of ScY01 in TR versus HSR as well as the HSR of the industrial strain versus a laboratory strain, our study revealed disparate response mechanisms of ScY01 during thermotolerant growth or under heat shock. In addition, through proteomics data-mining for decoding transcription factor interaction networks followed by validation experiments, we uncovered the functions of two novel transcription factors, Mig1 and Srb2, in enhancing the thermotolerance of the industrial strain. This study has demonstrated that accurate and high-throughput quantitative proteomics not only provides new insights into the molecular basis for complex microbial phenotypes but also pinpoints upstream regulators that can be targeted for improving the desired traits of industrial microorganisms.


Assuntos
Redes Reguladoras de Genes , Resposta ao Choque Térmico , Proteoma/análise , Saccharomyces cerevisiae/fisiologia , Termotolerância/genética , Fermentação , Complexo Mediador/fisiologia , Proteínas Repressoras/fisiologia , Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/análise , Proteínas de Saccharomyces cerevisiae/fisiologia , Especificidade da Espécie , Fatores de Tempo , Fatores de Transcrição
15.
J Proteome Res ; 16(2): 738-747, 2017 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-27995803

RESUMO

Proteomic analysis with data-independent acquisition (DIA) approaches represented by the sequential window acquisition of all theoretical fragment ion spectra (SWATH) technique has gained intense interest in recent years because DIA is able to overcome the intrinsic weakness of conventional data-dependent acquisition (DDA) methods and afford higher throughout and reproducibility for proteome-wide quantification. Although the raw mass spectrometry (MS) data quality and the data-mining workflow conceivably influence the throughput, accuracy and consistency of SWATH-based proteomic quantification, there lacks a systematic evaluation and optimization of the acquisition and data-processing parameters for SWATH MS analysis. Herein, we evaluated the impact of major acquisition parameters such as the precursor mass range, isolation window width and accumulation time as well as the data-processing variables including peak extraction criteria and spectra library selection on SWATH performance. Fine tuning these interdependent parameters can further improve the throughput and accuracy of SWATH quantification compared to the original setting adopted in most SWATH proteomic studies. Furthermore, we compared the effectiveness of two widely used peak extraction software PeakView and Spectronaut in discovery of differentially expressed proteins in a biological context. Our work is believed to contribute to a deeper understanding of the critical factors in SWATH MS experiments and help researchers optimize their SWATH parameters and workflows depending on the sample type, available instrument and software.


Assuntos
Processamento de Proteína Pós-Traducional/genética , Proteoma/genética , Proteômica/estatística & dados numéricos , Software , Cromatografia Líquida/estatística & dados numéricos , Mineração de Dados , Espectrometria de Massas em Tandem/métodos
16.
Chemosphere ; 356: 141853, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38582161

RESUMO

Ceftazidime (CAZ) is an emerging organic pollutant with a long-lasting presence in the environment. Although some PbO2 materials exhibit degradation capabilities, inefficient electron transport in the substrate layer and the problem of electrode stability still limit their use. Here, an interfacial design in which TiO2 nanotube arrays generate Ti3+ self-doping oxide substrate layers and highly active 3D Sb-SnO2 nanoflowers-like interlayers was used to prepare PbO2 anodes for efficient degradation of CAZ. Interestingly, after implementing Ti3+ self-doping in the PbO2 anode base layer and introducing 3D nanoflowers-like structures, the capacity for •OH generation increased significantly. The modified electrode exhibited 5-fold greater •OH generation capacity compared to the unmodified electrode, and a 2.7-fold longer accelerated electrode lifetime. The results indicate that interfacial engineering of the base and intermediate layers of the electrodes can improve the electron transfer efficiency, promote the formation of •OH, and extend the anode lifetime of the activated CAZ system.


Assuntos
Eletrodos , Chumbo , Nanotubos , Compostos de Estanho , Titânio , Titânio/química , Nanotubos/química , Compostos de Estanho/química , Chumbo/química , Óxidos/química , Antimônio/química , Técnicas Eletroquímicas/métodos , Poluentes Químicos da Água/química
17.
Virus Res ; 339: 199269, 2024 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-37952688

RESUMO

Cis-acting replication element (cre) is required for generating a diuridylylated VPg that acts as a protein primer to initiate the synthesis of picornaviral genome or antigenome. The cre is a stem-loop structure, dependent of different picornaviruses, located in different genomic regions. The AAACA motif is highly conserved in the apical loop of cre among several picornaviral members, and plays a key role in synthesizing a diuridylylated VPg. We previously demonstrated that senecavirus A (SVA) also possesses an AAACA-containing cre in its genome. Its natural cre (Nc), if functionally inactivated through site-directed mutagenesis (SDM), would confer a lethal impact on virus recovery, whereas an artificial cre (Ac) is able to compensate for the Nc-caused functional inactivation, leading to successful rescue of a viable SVA. In this study, we constructed a set of SVA cDNA clones. Each of them contained one functionally inactivated Nc, and an extra SDM-modified Ac. Every cDNA clone had a unique SDM-modified Ac. The test of virus recovery showed that only two SVAs were rescued from their individual cDNA clones. They were AAACU- and AAACC-containing Ac genotypes. Both viruses were serially passaged in vitro for analyzing their viral characteristics. The results showed that both AAACU and AAACC genotypes were genetically stable during twenty passages, implying when the Nc was functionally inactivated, SVA could still use an AAACH-containing Ac to complete its own replication cycle.


Assuntos
Picornaviridae , RNA Viral , Humanos , Sequência de Bases , RNA Viral/genética , DNA Complementar , Células HeLa , Conformação de Ácido Nucleico , Picornaviridae/genética , Replicação Viral/genética
18.
Mol Plant ; 17(1): 199-213, 2024 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-38018035

RESUMO

Protein phosphorylation regulates a variety of important cellular and physiological processes in plants. In-depth profiling of plant phosphoproteomes has been more technically challenging than that of animal phosphoproteomes. This is largely due to the need to improve protein extraction efficiency from plant cells, which have a dense cell wall, and to minimize sample loss resulting from the stringent sample clean-up steps required for the removal of a large amount of biomolecules interfering with phosphopeptide purification and mass spectrometry analysis. To this end, we developed a method with a streamlined workflow for highly efficient purification of phosphopeptides from tissues of various green organisms including Arabidopsis, rice, tomato, and Chlamydomonas reinhardtii, enabling in-depth identification with high quantitative reproducibility of about 11 000 phosphosites, the greatest depth achieved so far with single liquid chromatography-mass spectrometry (LC-MS) runs operated in a data-dependent acquisition (DDA) mode. The mainstay features of the method are the minimal sample loss achieved through elimination of sample clean-up before protease digestion and of desalting before phosphopeptide enrichment and hence the dramatic increases of time- and cost-effectiveness. The method, named GreenPhos, combined with single-shot LC-MS, enabled in-depth quantitative identification of Arabidopsis phosphoproteins, including differentially phosphorylated spliceosomal proteins, at multiple time points during salt stress and a number of kinase substrate motifs. GreenPhos is expected to serve as a universal method for purification of plant phosphopeptides, which, if samples are further fractionated and analyzed by multiple LC-MS runs, could enable measurement of plant phosphoproteomes with an unprecedented depth using a given mass spectrometry technology.


Assuntos
Arabidopsis , Animais , Arabidopsis/metabolismo , Fosfopeptídeos/análise , Fosfopeptídeos/química , Fosfopeptídeos/metabolismo , Espectrometria de Massas em Tandem/métodos , Reprodutibilidade dos Testes , Fosforilação , Fosfoproteínas/metabolismo
19.
Clin Rheumatol ; 43(3): 1073-1082, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38206544

RESUMO

OBJECTIVE: To assess the long-term safety and efficacy of umbilical cord mesenchymal stem cells transplantation (UMSCT) in patients with systemic sclerosis (SSc). METHODS: Forty-one patients with moderate to severe SSc underwent UMSCT at the Affiliated Drum Tower Hospital of Nanjing University Medical School from 2009 to 2017. In this study, we conducted a longitudinal and retrospective analysis and compared the clinical and laboratory manifestations before and after UMSCT. The main outcome of the study was overall survival. We evaluated changes in the modified Rodnan Skin Score (mRSS), as well as the changes in the pulmonary examination by using high-resolution computed tomography (HRCT) and ultrasound cardiogram (UCG). Additionally, we assessed the Health Assessment Questionnaire-Disability Index (HAQ-DI) and the severity of peripheral vascular involvement during the first year after treatment. RESULTS: The overall 5-year survival rate was 92.7% (38 out of 41 patients). Following UMSCT, the mean mRSS significantly decreased from 18.68 (SD = 7.26, n = 41) at baseline to 13.95 (SD = 8.49, n = 41), 13.29 (SD = 7.67, n = 38), and 12.39 (SD = 8.49, n = 38) at 1, 3, and 5 years, respectively. Improvement or stability in HRCT images was observed in 72.0% of interstitial lung disease (ILD) patients. Pulmonary arterial hypertension (PAH) remained stable in 5 out of 8 patients at the 5-year follow-up. No adverse events related to UMSCT were observed in any of the patients during the follow-up period. CONCLUSION: UMSCT may provide a safe and feasible treatment option for patients with moderate to severe SSc based on long-term follow-up data. The randomized controlled study will further confirm the clinical efficacy of UMSCT in SSc. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT00962923. Key Point • UMSCT is safe and effective for SSc patients.


Assuntos
Células-Tronco Mesenquimais , Escleroderma Sistêmico , Humanos , Seguimentos , Pulmão , Estudos Retrospectivos , Escleroderma Sistêmico/diagnóstico por imagem , Escleroderma Sistêmico/terapia
20.
Adv Sci (Weinh) ; 10(3): e2205054, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36437038

RESUMO

Chlorinated volatile organic compounds (CVOCs) are a class of hazardous pollutants that severely threaten environmental safety and human health. Although the catalytic oxidation technique for CVOCs elimination is effective, enhancing the catalytic efficiency and simultaneously inhibiting the production of organic byproducts is still of great challenge. Herein, Ru-substituted LaMn(Ru)O3+ δ perovskite with Ru-O-Mn structure and weakened Mn-O bond strength has been developed for catalytic oxidation of chlorobenzene (CB). The formed Ru-O-Mn structure serves as favorable sites for CB adsorption and activation, while the weakening of Mn-O bond strength facilitates the formation of active oxygen species and improves oxygen mobility and catalyst reducibility. Therefore, LaMn(Ru)O3+ δ exhibits superior low-temperature activity with the temperature of 90% CB conversion decreasing by over 90 °C compared with pristine perovskite, and the deep oxidation of chlorinated byproducts produced in low temperature is also accelerated. Furthermore, the introduction of water vapor into reaction system triggers the process of hydrolysis oxidation that promotes CB destruction and inhibits the generation of chlorinated byproducts, due to the higher-activity *OOH species generated from the dissociated H2 O reacting with adsorbed oxygen. This work can provide a unique, high-efficiency, and facile strategy for CVOCs degradation and environmental improvement.

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