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1.
Cell ; 187(13): 3319-3337.e18, 2024 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-38810645

RESUMO

The development of perennial crops holds great promise for sustainable agriculture and food security. However, the evolution of the transition between perenniality and annuality is poorly understood. Here, using two Brassicaceae species, Crucihimalaya himalaica and Erysimum nevadense, as polycarpic perennial models, we reveal that the transition from polycarpic perennial to biennial and annual flowering behavior is a continuum determined by the dosage of three closely related MADS-box genes. Diversification of the expression patterns, functional strengths, and combinations of these genes endows species with the potential to adopt various life-history strategies. Remarkably, we find that a single gene among these three is sufficient to convert winter-annual or annual Brassicaceae plants into polycarpic perennial flowering plants. Our work delineates a genetic basis for the evolution of diverse life-history strategies in plants and lays the groundwork for the generation of diverse perennial Brassicaceae crops in the future.


Assuntos
Brassicaceae , Flores , Regulação da Expressão Gênica de Plantas , Brassicaceae/genética , Brassicaceae/fisiologia , Produtos Agrícolas/genética , Flores/genética , Flores/fisiologia , Proteínas de Domínio MADS/genética , Proteínas de Domínio MADS/metabolismo , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Genoma de Planta , Fenômenos Fisiológicos Vegetais , Mapeamento Cromossômico , Mutação
2.
N Engl J Med ; 390(3): 230-241, 2024 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-38231624

RESUMO

BACKGROUND: Simnotrelvir is an oral 3-chymotrypsin-like protease inhibitor that has been found to have in vitro activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and potential efficacy in a phase 1B trial. METHODS: In this phase 2-3, double-blind, randomized, placebo-controlled trial, we assigned patients who had mild-to-moderate coronavirus disease 2019 (Covid-19) and onset of symptoms within the past 3 days in a 1:1 ratio to receive 750 mg of simnotrelvir plus 100 mg of ritonavir or placebo twice daily for 5 days. The primary efficacy end point was the time to sustained resolution of symptoms, defined as the absence of 11 Covid-19-related symptoms for 2 consecutive days. Safety and changes in viral load were also assessed. RESULTS: A total of 1208 patients were enrolled at 35 sites in China; 603 were assigned to receive simnotrelvir and 605 to receive placebo. Among patients in the modified intention-to-treat population who received the first dose of trial drug or placebo within 72 hours after symptom onset, the time to sustained resolution of Covid-19 symptoms was significantly shorter in the simnotrelvir group than in the placebo group (180.1 hours [95% confidence interval {CI}, 162.1 to 201.6] vs. 216.0 hours [95% CI, 203.4 to 228.1]; median difference, -35.8 hours [95% CI, -60.1 to -12.4]; P = 0.006 by Peto-Prentice test). On day 5, the decrease in viral load from baseline was greater in the simnotrelvir group than in the placebo group (mean difference [±SE], -1.51±0.14 log10 copies per milliliter; 95% CI, -1.79 to -1.24). The incidence of adverse events during treatment was higher in the simnotrelvir group than in the placebo group (29.0% vs. 21.6%). Most adverse events were mild or moderate. CONCLUSIONS: Early administration of simnotrelvir plus ritonavir shortened the time to the resolution of symptoms among adult patients with Covid-19, without evident safety concerns. (Funded by Jiangsu Simcere Pharmaceutical; ClinicalTrials.gov number, NCT05506176.).


Assuntos
COVID-19 , Inibidores de Protease de Coronavírus , Adulto , Humanos , Administração Oral , Antivirais/administração & dosagem , Antivirais/efeitos adversos , Antivirais/farmacologia , Antivirais/uso terapêutico , China , Proteínas M de Coronavírus/antagonistas & inibidores , Proteínas M de Coronavírus/metabolismo , Inibidores de Protease de Coronavírus/administração & dosagem , Inibidores de Protease de Coronavírus/efeitos adversos , Inibidores de Protease de Coronavírus/farmacologia , Inibidores de Protease de Coronavírus/uso terapêutico , COVID-19/metabolismo , COVID-19/terapia , Tratamento Farmacológico da COVID-19/métodos , Método Duplo-Cego , Ritonavir/administração & dosagem , Ritonavir/efeitos adversos , Ritonavir/farmacologia , Ritonavir/uso terapêutico , SARS-CoV-2/efeitos dos fármacos , Fatores de Tempo , Combinação de Medicamentos
3.
J Med Virol ; 96(6): e29736, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38864349

RESUMO

Although a range of blood traits have been reported to be associated with influenza A(H1N1)pdm09 (H1N1pdm09) disease severity, their underlying causal relationships and biological mechanisms have remained unclear. This study aimed to investigate the causal relationship between blood traits and H1N1pdm09 using a two-sample Mendelian randomization analysis. Based on the data from our in-house genome-wide association study (GWAS) on H1N1pdm09 disease severity (Ncase [severe] = 70, Ncontrol [mild] = 95) and GWAS summaries of 44 blood traits from Biobank Japan (N = 12 303-143 658), we identified the potential causal effect of blood traits on severe H1N1pdm09. The inverse variance weighted method analysis revealed significant causal effects of lower aspartate aminotransferase (AST, ß = -3.212, p = 0.019), low-density-lipoprotein cholesterol (LDL-C, ß = -1.372, p = 0.045), and basophil counts (Baso, ß = -1.638, p = 0.047) on severe H1N1pdm09 disease. Additionally, polygenic risk score analysis further confirmed genetic overlap between these blood traits and severe H1N1pdm09 disease. This study provided evidence linking the lower level of AST, LDL-C, and lower count of Baso with severe H1N1pdm09 disease, potentially identifying new therapeutic targets for patients with severe influenza.


Assuntos
Estudo de Associação Genômica Ampla , Vírus da Influenza A Subtipo H1N1 , Influenza Humana , Análise da Randomização Mendeliana , Humanos , Influenza Humana/virologia , Influenza Humana/genética , Influenza Humana/epidemiologia , Vírus da Influenza A Subtipo H1N1/genética , Japão/epidemiologia , Predisposição Genética para Doença , Índice de Gravidade de Doença , Polimorfismo de Nucleotídeo Único , Aspartato Aminotransferases/sangue , LDL-Colesterol/sangue , Ásia Oriental/epidemiologia , Povo Asiático/genética , População do Leste Asiático
4.
J Med Virol ; 96(1): e29338, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-38163280

RESUMO

Monkeypox (mpox), a viral zoonotic disease, is spreading worldwide. However, evidence that informs prevention and control strategies in the Asia Pacific Region is very limited. Our study aims to investigate the experiences of mpox patients from infection to treatment to provide scientific basis for the prevention and control. A multicenter qualitative design was used. A total of 15 mpox patients were recruited between July 6 and July 25, 2023, from six cities in China. Semistructured interviews were conducted by telephone and analyzed using the thematic analysis. The interview was divided into two sections: patients' experiences (prediagnosis experience, treatment-seeking experience, and quarantine experience) and advice. Prediagnosis experience was summarized into three themes: symptoms, possible routes of infection, and knowledge of mpox. Treatment-seeking experience was summarized into three themes: time of visit to hospital, diagnostic difficulties, and attitude toward diagnosis. Quarantine experience was summarized into three themes: body and mind reactions, reluctance to self-disclose infection status, and factors facilitating recovery. Themes identified from patients' advice were as follows: (1) Increase in testing channels and methods, (2) Development and introduction of vaccines, (3) Adjustment of quarantine program, (4) Improvement of treatment measures, and (5) Improvement of publicity and education. To effectively curb the mpox epidemic, structured measures are urgently needed to address the mpox-related stigma and discrimination. Targeted health education should be provided to MSM, focusing on the prevention, detection, and treatment services. Hospitals should enhance the training of clinicians in key departments including infectious disease and dermatology, to improve diagnostic capability and sensitivity. Furthermore, given the absence of specific antiviral medications, supervised home quarantine may be a good option.


Assuntos
Mpox , Humanos , China/epidemiologia , Ásia , Antivirais , Cidades
5.
Virol J ; 21(1): 3, 2024 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-38178224

RESUMO

BACKGROUND: International migration has accelerated the HIV-1 spread across national borders, gradually reducing the restrictions on the geographical distribution of HIV-1 subtypes. Subtypes A and G are globally recognized as the third and sixth most dominant HIV-1 genotypes, mainly prevalent in Africa, but rarely detected in China. Here we reported an imported HIV-1 recombinant which was composed of sub-subtypes A1 and A7 of subtype A and subtype G genes in a Chinese female. This virus was the first HIV-1 recombinant including A7 genes reported in the world. CASE PRESENTATION: The near full-length genome (NFLG) was obtained from the plasma sample of the female in an HIV-1 molecular epidemiological survey with 853 participants in China. Phylogenetic analyses showed that this NFLG sequence contains three A7 segments, four G segments and one A1 segment with seven breakpoints, and all these segments were closely related to HIV-1 references circulating in Africa. The evidence from epidemiological investigation indicated that this female participant had a more-than-two-years heterosexual contact history with a fixed partner from Nigeria, a country in west Africa, which further supported the results of phylogenetic analyses. By the Bayesian phylogenetic analyses, the times of most recent common ancestors (tMRCA) of the partial pol gene (nt2308-3284, A7 region) and full-length vpr-vpu plus partial env gene (nt5534-6858, G region) were estimated around 1989 and 1984, respectively. CONCLUSIONS: In this study, by using the NFLG sequencing, we identified an imported HIV-1 A1/A7/G recombinant which was estimated to originate around 1980s in Africa and introduced into China with international migration. This study highlighted the complexity of the global HIV-1 epidemic, the necessity of using genome sequences to determine HIV-1 genotypes and the importance of real-time monitoring of HIV-1 infection among international migrants and travelers.


Assuntos
Soropositividade para HIV , HIV-1 , Humanos , Feminino , HIV-1/genética , Filogenia , Teorema de Bayes , China/epidemiologia , Nigéria
6.
J Immunol ; 208(11): 2515-2522, 2022 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-35534212

RESUMO

The cannabinoid receptor 2 (CB2) is a receptor mainly expressed in immune cells and believed to be immunosuppressive in infective or inflammatory models. However, its role in sepsis has not been fully elucidated. In this study, we delineate the function and mechanism of CB2 in the cecal ligation and puncture-induced septic model in mice. The activation of CB2 signaling with HU308 led to decreased survival rates and more severe lung injury in septic mice, and lower IL-10 levels in peritoneal lavage fluid were observed in the CB2 agonist group. The mice with conditional knockout of CB2-encoding gene CNR2 in CD4+ T cells (CD4 Cre CNR2fl/fl) improved survival, enhanced IL-10 production, and ameliorated pulmonary damage in the sepsis model after CB2 activation. In addition, double-knockout of the CNR2 gene (Lyz2 Cre CD4 Cre CNR2fl/fl) decreased the susceptibility to sepsis compared with Lyz2 Cre CNR2fl/fl mice. Mechanistically, the blockade of IL-10 with the anti-IL-10 Ab abolished its protection in CD4 Cre CNR2fl/fl mice. In accordance with the animal study, in vitro results revealed that the lack of CNR2 in CD4+ cells elevated IL-10 production, and CB2 activation inhibited CD4+ T cell-derived IL-10 production. Furthermore, in the clinical environment, septic patients expressed enhanced CB2 mRNA levels compared with healthy donors in PBMCs, and their CB2 expression was inversely correlated with IL-10. These results suggested that the activation of CD4+ T cell-derived CB2 increased susceptibility to sepsis through inhibiting IL-10 production.


Assuntos
Linfócitos T CD4-Positivos , Interleucina-10 , Receptor CB2 de Canabinoide , Sepse , Animais , Ligadura , Camundongos , Camundongos Endogâmicos C57BL , Receptor CB2 de Canabinoide/genética , Sepse/patologia
7.
Mol Breed ; 44(4): 27, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38525006

RESUMO

QuerySeed germination is a vital step in the life cycle of a plant, playing a significant role in seedling establishment and crop yield potential. It is also an important factor in the conservation of plant germplasm resources. This complex process is influenced by a myriad of factors, including environmental conditions, the genetic makeup of the seed, and endogenous hormones. The perception of these environmental signals triggers a cascade of intricate signal transduction events that determine whether a seed germinates or remains dormant. Despite considerable progress in uncovering the molecular mechanisms governing these processes, many questions remain unanswered. In this review, we summarize the current progress in the molecular mechanisms underlying the perception of environmental signals and consequent signal transduction during seed germination, and discuss questions that need to be addressed to better understand the process of seed germination and develop novel strategies for germplasm improvement.

8.
BMC Public Health ; 24(1): 1445, 2024 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-38816790

RESUMO

OBJECTIVE: To describe how mental health and sleep status influence the health-related quality of life (HRQOL) of people living with HIV/AIDS (PLWHA) during the novel coronavirus disease 2019 (COVID-19) pandemic, and to apply targeted interventions to improve the HRQOL. METHODS: A web-based online questionnaire survey was administered. Descriptive analysis was used to depict the mental health and sleep status. Correlation analysis and the structural equation model (SEM) method were used to analyze the influence of mental health and sleep status on HRQOL in PLWHA. RESULTS: After excluding 24 unqualified questionnaires, a total of 490 participants in this survey were included in the statistical analysis. Of the participants, 66.1% and 55.1% reported mild or worse symptoms of depression and anxiety, respectively. Overall, 70.0% had varying degrees of sleep problems. Correlation analysis showed that anxiety had the strongest correlation with sleep disturbances and sleep quality (R = 0.588 and 0.551, respectively), while depression had the strongest correlation with the HRQOL psychological and physical domains (R = - 0.759 and - 0.682, respectively). SEM analysis showed that depression, sleep quality, and psychological domains had the greatest item load on mental health, sleep status, and HRQOL (093, 0.82, and 0.89, respectively). Mental health had a more significant influence than sleep status on HRQOL, as indicated by factor loading (- 0.75 and - 0.15, respectively). CONCLUSIONS: There were more severe mental health and sleep problems among PLWHA during the COVID-19 pandemic, thus, mental health intervention, especially to relieve depression symptoms, may be the most important approach to improve the HRQOL among PLWHA.


Assuntos
COVID-19 , Infecções por HIV , Saúde Mental , Qualidade de Vida , Transtornos do Sono-Vigília , Humanos , COVID-19/psicologia , COVID-19/epidemiologia , Qualidade de Vida/psicologia , Masculino , Feminino , Infecções por HIV/psicologia , Infecções por HIV/epidemiologia , Adulto , Pessoa de Meia-Idade , China/epidemiologia , Transtornos do Sono-Vigília/epidemiologia , Transtornos do Sono-Vigília/psicologia , Depressão/epidemiologia , Depressão/psicologia , Inquéritos e Questionários , Ansiedade/epidemiologia , Ansiedade/psicologia , Qualidade do Sono , Pandemias , População do Leste Asiático
9.
Plant Mol Biol ; 111(4-5): 415-428, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-36867321

RESUMO

Prolonged storage of rice seeds can lead to a decrease in seed vigor and seedling quality. The Lipoxygenase (LOX) gene family is widely distributed in plants, and LOX activity is closely related to seed viability and stress tolerance. In this study, the lipoxygenase OsLOX10 gene from the 9-lipoxygenase metabolic pathway was cloned from rice, and its roles in determining seed longevity and tolerance to saline-alkaline stress caused by Na2CO3 in rice seedlings were mainly investigated. CRISPR/Cas9 knockout of OsLOX10 increased seed longevity compared with the wild-type and OsLOX10 overexpression lines in response to artificial aging. The expression levels of other 9-lipoxygenase metabolic pathway related genes, such as LOX1, LOX2 and LOX3, were increased in the LOX10 overexpression lines. Quantitative real-time PCR and histochemical staining analysis showed that the expression of LOX10 was highest in seed hulls, anthers and the early germinating seeds. KI-I2 staining of starch showed that LOX10 could catalyze the degradation of linoleic acid. Furthermore, we found that the transgenic lines overexpressing LOX10 showed better tolerance to saline-alkaline stress than the wild-type and knockout mutant lines. Overall, our study demonstrated that the knockout LOX10 mutant increased seed longevity, whereas overexpression of LOX10 enhanced tolerance to saline-alkaline stress in rice seedlings.


Assuntos
Lipoxigenase , Oryza , Lipoxigenase/genética , Plântula/metabolismo , Oryza/genética , Longevidade , Sementes/genética
10.
EMBO J ; 38(8)2019 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-30842098

RESUMO

Heteroblasty refers to a phenomenon that a plant produces morphologically or functionally different lateral organs in an age-dependent manner. In the model plant Arabidopsis thaliana, the production of trichomes (epidermal leaf hairs) on the abaxial (lower) side of leaves is a heteroblastic mark for the juvenile-to-adult transition. Here, we show that the heteroblastic development of abaxial trichomes is regulated by a spatiotemporally regulated complex comprising the leaf abaxial fate determinant (KAN1) and the developmental timer (miR172-targeted AP2-like proteins). We provide evidence that a short-distance chromatin loop brings the downstream enhancer element into close association with the promoter elements of GL1, which encodes a MYB transcription factor essential for trichome initiation. During juvenile phase, the KAN1-AP2 repressive complex binds to the downstream sequence of GL1 and represses its expression through chromatin looping. As plants age, the gradual reduction in AP2-like protein levels leads to decreased amount of the KAN1-AP2 complex, thereby licensing GL1 expression and the abaxial trichome initiation. Our results thus reveal a novel molecular mechanism by which a heteroblastic trait is governed by integrating age and leaf polarity cue in plants.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/crescimento & desenvolvimento , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Folhas de Planta/crescimento & desenvolvimento , Regiões Promotoras Genéticas , Análise Espaço-Temporal , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , MicroRNAs/genética , Mutação , Fenótipo , Folhas de Planta/genética , Folhas de Planta/metabolismo , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/crescimento & desenvolvimento , Plantas Geneticamente Modificadas/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Ativação Transcricional
11.
J Med Virol ; 95(1): e28106, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36039848

RESUMO

The discovery of broadly neutralizing monoclonal antibodies against influenza viruses has raised hope for the successful development of new antiviral drugs. However, due to the speed and variety of mutations in influenza viruses, single-component antibodies that recognize specific epitopes are susceptible to viral escape and have limited efficacy when administration is delayed. Hence, it is necessary to develop alternative strategies with better antiviral activity. Influenza B virus infection can cause severe illness in children and the elderly. Commonly used anti-influenza drugs have low clinical efficacy against influenza B virus. In this study, we investigated the antiviral efficacy of combinations of representative monoclonal antibodies targeting different antigenic epitopes against the influenza B virus. We found that combinations of antibodies recognizing the hemagglutinin (HA) head and stem regions showed a stronger neutralizing activity than single antibodies and other antibody combinations in vitro. In addition, we found that pair-wise combinations of antibodies recognizing the HA head region, HA stem region, and neuraminidase enzyme-activated region showed superior antiviral activity than single antibodies in both mouse and ferret in vivo protection assays. Notably, these antibody combinations still displayed good antiviral efficacy when treatment was delayed. Mechanistic studies further revealed that combining antibodies recognizing different epitope regions resulted in extremely strong antibody-dependent cell-mediated cytotoxicity, which may partly explain their superior antiviral effects. Together, the findings of this study provide new avenues for the development of better antiviral drugs and vaccines against influenza viruses.


Assuntos
Vacinas contra Influenza , Influenza Humana , Infecções por Orthomyxoviridae , Animais , Camundongos , Humanos , Epitopos , Vírus da Influenza B , Anticorpos Neutralizantes , Anticorpos Antivirais , Anticorpos Amplamente Neutralizantes , Glicoproteínas de Hemaglutininação de Vírus da Influenza/genética , Furões , Hemaglutininas , Anticorpos Monoclonais/uso terapêutico , Antivirais/farmacologia , Antivirais/uso terapêutico
12.
J Med Virol ; 95(10): e29198, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37881113

RESUMO

Human mpox is occurring worldwide, however, evidence from the Asian Pacific Region is limited. In this multicenter cross-sectional study, information of confirmed mpox cases diagnosed between June 1 and July 31, 2023 in China. Information included demographic and epidemiological characteristics, and clinical manifestations, laboratory results, and mental health status of mpox cases. A total of 115 confirmed mpox cases were enrolled. All cases were men. A total of 102 (90.3%) identified as homosexual. The median age was 31.0 years (interquartile range 27.0-36.5). A total of 65 (56.5%) were HIV-positive, of whom 92.3% were receiving antiretroviral therapy (ART). A total of 19/39 (40.4%) had a CD4 cell count <500 cells/µL. Systemic features such as fever (73.0%), lymphadenopathies (49.6%), and myalgia (28.7%) were commonly observed. Skin lesions were present in all participants: 49.6% in the genital area and 27.0% in the perianal area. Vesicular rash (78.3%) and papular rash (44.3%) were the most common lesion morphologies. People living with HIV were more likely to have anxiety than those living without HIV. The majority of mpox cases had primary genital lesions and sexual activities before diagnosis, which supports the likelihood of sexual contact transmission. Guidelines on hospitalization and isolation protocols for mpox patients necessitate further confirmation.


Assuntos
Exantema , Infecções por HIV , Mpox , Adulto , Humanos , Masculino , China/epidemiologia , Estudos Transversais , Nível de Saúde , Infecções por HIV/tratamento farmacológico , Infecções por HIV/epidemiologia
13.
Analyst ; 148(19): 4746-4752, 2023 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-37646283

RESUMO

Sensitive detection of tumor necrosis factor-alpha (TNF-α) in human serum is beneficial for finding cancer patients early due to overexpressed TNF-α being related to some cancers. Here, a photoelectrochemical (PEC) aptasensor was constructed for ultrasensitive TNF-α assay based on the signal generator of hollow CdS cubes (H-CdS) and the signal extinguishing activity of NiCo2O4-Au. In this work, compared with traditional solid CdS, H-CdS could greatly promote the PEC signal because its hollow structure could accelerate the separation of photogenerated charges, which also possesses abundant active sites and high light absorption capability. Moreover, H-CdS can be prepared facilely with Cd-based Prussian blue analogs as the precursor. Meanwhile, NiCo2O4-Au was fabricated and utilized as a signal extinguisher. In the presence of TNF-α, NiCo2O4-Au could be introduced onto the H-CdS modified electrode, producing competitive consumption of the electron donor effect, the p-n semiconductor quenching effect, and the mimetic enzymatic catalytic precipitation effect, which all can significantly reduce the PEC signal. Based on the signal extinguishing activity of NiCo2O4-Au and the signal generator of H-CdS, TNF-α can be detected sensitively with a lower detection limit (0.63 fg mL-1) and a wide linear range (1 fg mL-1- to 1 ng mL-1), which may have a potential application in the PEC bioanalysis field and the disease diagnostics field.


Assuntos
Bioensaio , Fator de Necrose Tumoral alfa , Humanos , Catálise , Eletrodos , Semicondutores
14.
BMC Genomics ; 23(Suppl 1): 272, 2022 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-35392802

RESUMO

BACKGROUND: Transcription factors (TFs) play central roles in regulating gene expression. With the rapid growth in the use of high-throughput sequencing methods, there is a need to develop a comprehensive data processing and analyzing framework for inferring influential TFs based on ChIP-seq/ATAC-seq datasets. RESULTS: Here, we introduce FindIT2 (Find Influential TFs and Targets), an R/Bioconductor package for annotating and processing high-throughput multi-omics data. FindIT2 supports a complete framework for annotating ChIP-seq/ATAC-seq peaks, identifying TF targets by the combination of ChIP-seq and RNA-seq datasets, and inferring influential TFs based on different types of data input. Moreover, benefited from the annotation framework based on Bioconductor, FindIT2 can be applied to any species with genomic annotations, which is particularly useful for the non-model species that are less well-studied. CONCLUSION: FindIT2 provides a user-friendly and flexible framework to generate results at different levels according to the richness of the annotation information of user's species. FindIT2 is compatible with all the operating systems and is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor ( https://bioconductor.org/packages/devel/bioc/html/FindIT2.html ).


Assuntos
Software , Fatores de Transcrição , Sequenciamento de Cromatina por Imunoprecipitação , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Fatores de Transcrição/genética
15.
Anal Biochem ; 645: 114605, 2022 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-35181297

RESUMO

Kynurenine (Kyn) is involved in a variety of physiological/pathological reactions via activating aryl hydrocarbon receptor (Ahr). However, how to activate Ahr by Kyn under physiological/pathological conditions is still unclear. Here, we presented that Kyn (8 µM, a concentration less than the dose of Kyn-induced Ahr activation) significantly induced the nuclear transfer of Ahr and the expression of cytochrome P450 1A1 (CYP1A1, a classic biomarker for Ahr activation) when co-administered with ultraviolet (UV) irradiation in 95D cells, which were transfected transiently with siRNA against indoleamine 2,3-dioxygenase 1 (IDO 1) and cultured in cell medium supplemented with bovine serum containing bovine serum albumin (BSA), in vitro. Additionally, we found that the fluorescence intensity of BSA was attenuated by Kyn (2, 4, 6, 8, 10, 12 and 14 µM) mainly through quenching the fluorescence of tryptophan (Trp) residues in the pattern of dynamic quenching related to molecular diffusion. More important, resonance energy transfer from excited-state BSA to Kyn was confirmed, leading to the generation "energetic" Kyn that might be ability of hyperactivity according to the theory of photochemical reaction. These data indicate that UV irradiation is contributable for Kyn to function, and present a novel pattern of altering the activity of biomolecules to some degree.


Assuntos
Indolamina-Pirrol 2,3,-Dioxigenase , Cinurenina , Transferência de Energia , Indolamina-Pirrol 2,3,-Dioxigenase/genética , Indolamina-Pirrol 2,3,-Dioxigenase/metabolismo , Cinurenina/metabolismo , Cinurenina/farmacologia , Triptofano/metabolismo
16.
Neurol Sci ; 43(6): 4045-4048, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35355146

RESUMO

INTRODUCTION: As acquired immunodeficiency syndrome (AIDS) becomes more widespread, there will be an increasing need for diagnostic AIDS-related neurological syndromes. AIDS-related myelitis is easy to be ignored, and AIDS-related longitudinal myelitis has not yet been reported. CASE PRESENTATION: A 45-year-old male patient was admitted to our hospital after 3 days of progressive slurred speech and limb weakness. Neurologic examination revealed near-complete four-limb paralysis with dyspnea, dysarthria, and neck rigidity. Contrast-enhanced T2-weighted magnetic resonance imaging showed hyperintensities within the entire spinal cord. Cerebrospinal fluid analysis showed elevated white blood cell count and protein level. He was administered high-dose immunoglobulin and methylprednisolone. There was rapid regression in his symptoms after a month of therapy. CONCLUSIONS: This unique presentation of AIDS with longitudinal myelitis involving the entire spinal cord enriches our understanding of the clinical spectrum of this condition. Our case provides essential information for the diagnosis and treatment of longitudinal myelitis in AIDS patients.


Assuntos
Síndrome da Imunodeficiência Adquirida , Mielite , Síndrome da Imunodeficiência Adquirida/complicações , Humanos , Imageamento por Ressonância Magnética , Masculino , Pessoa de Meia-Idade , Mielite/diagnóstico por imagem , Mielite/tratamento farmacológico , Paralisia , Medula Espinal/diagnóstico por imagem
17.
J Ind Microbiol Biotechnol ; 49(4)2022 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-35648451

RESUMO

D, D-carboxypeptidase DacA plays an important role in the synthesis and stabilization of Escherichia coli cell wall peptidoglycan. The production level of extracellular recombinant proteins in E. coli can be enhanced by high D, D-carboxypeptidase activity. Construction of expression systems under optimal promoters is one of the main strategies to realize high protein production in E. coli. In this study, the promoter PdacA-3 from DacA on the genome of E. coli BL21 (DE3) was verified to be efficient for recombinant green fluorescent protein using the plasmid mutant pET28a-PdacA with PdacA-3. Meanwhile, the promoter PdacA-3 was engineered to increase the production level of proteins via inserting one or two Shine-Dalgarno (SD) sequences between the promoter PdacA-3 and the target genes. The expression level of dacA on the genome was increased by the improved transcription of the engineered promoters (especially after inserting one additional SD sequence). The engineered promoters increased cell membrane permeabilities to significantly enhance the secretion production of extracellular recombinant proteins in E. coli. Among them, the extracellular recombinant amylase activities in E. coli BL21::1SD-pET28a-amyK and E. coli BL21::2SD-pET28a-amyK were increased by 2.0- and 1.6-fold that of the control (E. coli BL21-pET28a-amyK), respectively. Promoter engineering also affected the morphology and growth of the E. coli mutants. It was indicated that the engineered promoters enhanced the expression of dacA on the genome to disturb the synthesis and structural stability of cell wall peptidoglycans.


Assuntos
Escherichia coli , Peptidoglicano , Carboxipeptidases , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Fluorescência Verde/genética , Proteínas de Fluorescência Verde/metabolismo , Peptidoglicano/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo
18.
BMC Plant Biol ; 21(1): 287, 2021 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-34167489

RESUMO

BACKGROUND: Phosphoenolpyruvate carboxylase (PEPC) plays an important role in the primary metabolism of higher plants. Several studies have revealed the critical importance of PEPC in the interaction of carbon and nitrogen metabolism. However, the function mechanism of PEPC in nitrogen metabolism is unclear and needs further investigation. RESULTS: This study indicates that transgenic rice expressing the sugarcane C4-PEPC gene displayed shorter primary roots and fewer crown roots at the seedling stage. However, total nitrogen content was significantly higher in transgenic rice than in wild type (WT) plants. Proteomic analysis revealed that there were more differentially expressed proteins (DEPs) responding to nitrogen changes in transgenic rice. In particular, the most enriched pathway "glutathione (GSH) metabolism", which mainly contains GSH S-transferase (GST), was identified in transgenic rice. The expression of endogenous PEPC, GST and several genes involved in the TCA cycle, glycolysis and nitrogen assimilation changed in transgenic rice. Correspondingly, the activity of enzymes including GST, citrate synthase, 6-phosphofructokinase, pyruvate kinase and ferredoxin-dependent glutamate synthase significantly changed. In addition, the levels of organic acids in the TCA cycle and carbohydrates including sucrose, starch and soluble sugar altered in transgenic rice under different nitrogen source concentrations. GSH that the substrate of GST and its components including glutamic acid, cysteine and glycine accumulated in transgenic rice. Moreover, the levels of phytohormones including indoleacetic acid (IAA), zeatin (ZT) and isopentenyladenosine (2ip) were lower in the roots of transgenic rice under total nutrients. Taken together, the phenotype, physiological and biochemical characteristics of transgenic rice expressing C4-PEPC were different from WT under different nitrogen levels. CONCLUSIONS: Our results revealed the possibility that PEPC affects nitrogen metabolism through regulating GST, which provide a new direction and concepts for the further study of the PEPC functional mechanism in nitrogen metabolism.


Assuntos
Glutationa Transferase/metabolismo , Nitrogênio/metabolismo , Oryza/enzimologia , Fosfoenolpiruvato Carboxilase/metabolismo , Saccharum/enzimologia , Carbono/metabolismo , Oryza/genética , Oryza/metabolismo , Fosfoenolpiruvato Carboxilase/genética , Plantas Geneticamente Modificadas , Proteômica , Saccharum/genética , Transcriptoma
19.
Inorg Chem ; 2021 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-34296855

RESUMO

Developing high-performance catalysts toward the Fenton reaction is important for environmental protection and sustainable development, yet it is still challenging. The high-spin states of first-row transition metal atoms with tetrahedral coordination provide a flexible electronic environment to activate the catalyst and elevate its catalytic activity. As a type of material with adjustable structures, metal-organic frameworks (MOFs) are excellent candidate catalysts as they can accurately regulate the coordination configurations of metal ions. In this paper, we investigate and summarize the direct formation of bimetallic carboxylate Li/Co-MOFs with tetrahedral coordination metal centers in a mixed H2O/polar organic solvent system. The induction of Li(I) ions is manifested in the generation of hydroxides during the dissociation of the Co(II) solvation structure to trigger the tetrahedral coordination behavior of Co(II). These Li/Co-MOFs containing high-spin Co(II) centers can serve as highly efficient Fenton-like catalysts for organics. This study provides a promising strategy for rational design of MOF-based catalysts with high-spin metal centers for application in environment governance.

20.
J Allergy Clin Immunol ; 146(1): 119-127.e4, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32360286

RESUMO

BACKGROUND: The outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 was first reported in Wuhan, December 2019, and continuously poses a serious threat to public health, highlighting the urgent need of identifying biomarkers for disease severity and progression. OBJECTIVE: We sought to identify biomarkers for disease severity and progression of COVID-19. METHODS: Forty-eight cytokines in the plasma samples from 50 COVID-19 cases including 11 critically ill, 25 severe, and 14 moderate patients were measured and analyzed in combination with clinical data. RESULTS: Levels of 14 cytokines were found to be significantly elevated in COVID-19 cases and showed different expression profiles in patients with different disease severity. Moreover, expression levels of IFN-γ-induced protein 10, monocyte chemotactic protein-3, hepatocyte growth factor, monokine-induced gamma IFN, and macrophage inflammatory protein 1 alpha, which were shown to be highly associated with disease severity during disease progression, were remarkably higher in critically ill patients, followed by severe and then the moderate patients. Serial detection of the 5 cytokines in 16 cases showed that continuously high levels were associated with deteriorated progression of disease and fatal outcome. Furthermore, IFN-γ-induced protein 10 and monocyte chemotactic protein-3 were excellent predictors for the progression of COVID-19, and the combination of the 2 cytokines showed the biggest area under the curve of the receiver-operating characteristics calculations with a value of 0.99. CONCLUSIONS: In this study, we report biomarkers that are highly associated with disease severity and progression of COVID-19. These findings add to our understanding of the immunopathologic mechanisms of severe acute respiratory syndrome coronavirus 2 infection, and provide potential therapeutic targets and strategies.


Assuntos
Biomarcadores/sangue , Quimiocina CCL7/sangue , Quimiocina CXCL10/sangue , Infecções por Coronavirus/sangue , Pneumonia Viral/sangue , Adulto , Idoso , Betacoronavirus , COVID-19 , Estado Terminal , Citocinas/sangue , Progressão da Doença , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Pandemias , SARS-CoV-2 , Adulto Jovem
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