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1.
Sci Total Environ ; 946: 174245, 2024 Oct 10.
Artículo en Inglés | MEDLINE | ID: mdl-38925395

RESUMEN

Dissolved organic matter (DOM) plays an important role in governing metal speciation and migration in aquatic systems. In this study, various DOM samples were collected from Lakes Erhai, Kokonor, and Chaka, and size-fractionated into high molecular weight (HMW, 1 kDa-0.7 µm) and low molecular weight (LMW, <1 kDa) fractions for measurements of dissolved organic carbon (DOC), spectral properties, and metal binding behaviors. Our results demonstrated that samples from Lake Chaka exhibited the highest DOC concentration and fluorescence indices but the lowest percentage of carbohydrates. Regardless of sampling locations, the HMW-DOM fractions contained higher abundances of aromatic DOM, carbohydrates and protein-like substances, but lower abundance of fulvic acid-like substances compared to those in the LMW fractions. Metal titration experiments coupled with the excitation-emission matrix (EEM)-parallel factor (PARAFAC) modeling revealed that the quenching of the PARAFAC-derived fluorescent components was more pronounced in the presence of Cu(II) compared to Pb(II). Humic-like components emerged as a superior model, exhibiting higher binding affinities for Cu(II) than protein-like substances, while the opposite trend was observed for Pb(II). In samples obtained from Lakes Erhai and Kokonor, the condition stability constants (Log KM) for the binding of both Cu(II) and Pb(II) with the HMW-DOM fraction were higher than those with the LMW-DOM fraction. Conversely, a contrasting trend was observed for Lake Chaka. This study highlighted the heterogeneity in spectral properties and metal-binding behaviors of natural DOMs, contributing to an improved understanding of the molecular interactions between DOM components and metal ions and their environmental fate in aquatic ecosystems.

2.
Gut Microbes ; 16(1): 2367297, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38899956

RESUMEN

The gut fungi play important roles in human health and are involved in energy metabolism. This study aimed to examine gut mycobiome composition in obese subjects in two geographically different regions in China and to identify specific gut fungi associated with obesity. A total of 217 subjects from two regions with different urbanization levels [Hong Kong (HK): obese, n = 59; lean, n = 59; Kunming (KM): obese, n = 50; lean, n = 49. Mean body mass index (BMI) for obesity = 33.7] were recruited. We performed deep shotgun metagenomic sequencing on fecal samples to compare gut mycobiome composition and trophic functions in lean and obese subjects across these two regions. The gut mycobiome of obese subjects in both HK and KM were altered compared to those of lean subjects, characterized by a decrease in the relative abundance of Nakaseomyces, Schizosaccharomyces pombe, Candida dubliniensis and an increase in the abundance of Lanchanceathermotolerans, Saccharomyces paradox, Parastagonospora nodorum and Myceliophthorathermophila. Reduced fungal - bacterial and fungal - fungal correlations as well as increased negative fungal-bacterial correlations were observed in the gut of obese subjects. Furthermore, the anti-obesity effect of fungus S. pombe was further validated using a mouse model. Supplementing high-fat diet-induced obese mice with the fungus for 12 weeks led to a significant reduction in body weight gain (p < 0.001), and an improvement in lipid and glucose metabolism compared to mice without intervention. In conclusion, the gut mycobiome composition and functionalities of obese subjects were altered. These data shed light on the potential of utilizing fungus-based therapeutics for the treatment of obesity. S. pombe may serve as a potential fungal probiotic in the prevention of diet-induced obesity and future human trials are needed.


Asunto(s)
Heces , Hongos , Microbioma Gastrointestinal , Micobioma , Obesidad , Obesidad/microbiología , Humanos , Animales , Hongos/clasificación , Hongos/aislamiento & purificación , Hongos/genética , Masculino , Ratones , China , Femenino , Heces/microbiología , Adulto , Bacterias/clasificación , Bacterias/aislamiento & purificación , Bacterias/genética , Persona de Mediana Edad , Ratones Endogámicos C57BL , Índice de Masa Corporal
3.
Int J Cancer ; 155(7): 1327-1339, 2024 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-38738976

RESUMEN

The primary objective of this study is to develop a prediction model for peritoneal metastasis (PM) in colorectal cancer by integrating the genomic features of primary colorectal cancer, along with clinicopathological features. Concurrently, we aim to identify potential target implicated in the peritoneal dissemination of colorectal cancer through bioinformatics exploration and experimental validation. By analyzing the genomic landscape of primary colorectal cancer and clinicopathological features from 363 metastatic colorectal cancer patients, we identified 22 differently distributed variables, which were used for subsequent LASSO regression to construct a PM prediction model. The integrated model established by LASSO regression, which incorporated two clinicopathological variables and seven genomic variables, precisely discriminated PM cases (AUC 0.899; 95% CI 0.860-0.937) with good calibration (Hosmer-Lemeshow test p = .147). Model validation yielded AUCs of 0.898 (95% CI 0.896-0.899) and 0.704 (95% CI 0.622-0.787) internally and externally, respectively. Additionally, the peritoneal metastasis-related genomic signature (PGS), which was composed of the seven genes in the integrated model, has prognostic stratification capability for colorectal cancer. The divergent genomic landscape drives the driver genes of PM. Bioinformatic analysis concerning these driver genes indicated SERINC1 may be associated with PM. Subsequent experiments indicate that knocking down of SERINC1 functionally suppresses peritoneal dissemination, emphasizing its importance in CRCPM. In summary, the genomic landscape of primary cancer in colorectal cancer defines peritoneal metastatic pattern and reveals the potential target of SERINC1 for PM in colorectal cancer.


Asunto(s)
Neoplasias Colorrectales , Genómica , Neoplasias Peritoneales , Humanos , Neoplasias Peritoneales/secundario , Neoplasias Peritoneales/genética , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/patología , Femenino , Masculino , Persona de Mediana Edad , Genómica/métodos , Pronóstico , Biomarcadores de Tumor/genética , Anciano , Animales , Regulación Neoplásica de la Expresión Génica , Ratones , Biología Computacional/métodos
4.
Virus Res ; 346: 199396, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38763299

RESUMEN

Porcine circovirus type 2 (PCV2) infection leads to multi-system inflammation in pigs, and this effect can be achieved by upregulating host miR-21. The underlying mechanism of miR-21 regulates PCV2-induced inflammation is already known, however, how PCV2 regulates miR-21 levels and function using both autonomic and host factors remains to be further revealed. Here we present the first evidence that PCV2 ORF5 induces an inflammatory response by up-regulating miR-21 level through targeting nuclear miR-30d. In this study, we found that overexpression of ORF5 significantly increased miR-21 level and promoted the expression of inflammatory cytokines and activation of the NF-κB pathway, while ORF5 mutation had the opposite effect. Moreover, the differential expression of miR-21 could significantly change the pro-inflammatory effect of ORF5, indicating that ORF5 promotes inflammatory response by up-regulating miR-21. Bioinformatics analysis and clinical detection found that nuclear miR-30d was significantly down-regulated after ORF5 overexpression and PCV2 infection, and targeted pri-miR-21 and PCV2 ORF5. Functionally, we found that miR-30d inhibited the levels of miR-21 and inflammatory cytokines in cells. Mechanistically, we demonstrated that ORF5 inhibits miR-30d expression levels through direct binding but not via the circRNA pathway, and miR-30d inhibits miR-21 levels by targeting pri-miR-21. In summary, the present study revealed the molecular mechanism of ORF5 upregulation of miR-21, further refined the molecular chain of PCV2-induced inflammatory response and elucidated the role of miRNAs in it.


Asunto(s)
Infecciones por Circoviridae , Circovirus , Inflamación , MicroARNs , Regulación hacia Arriba , Circovirus/genética , Circovirus/fisiología , MicroARNs/genética , MicroARNs/metabolismo , Animales , Porcinos , Infecciones por Circoviridae/virología , Infecciones por Circoviridae/veterinaria , Infecciones por Circoviridae/genética , Inflamación/genética , Enfermedades de los Porcinos/virología , Enfermedades de los Porcinos/genética , Citocinas/metabolismo , Citocinas/genética , Línea Celular , Interacciones Huésped-Patógeno , FN-kappa B/metabolismo , FN-kappa B/genética , Proteínas Virales/genética , Proteínas Virales/metabolismo
5.
Microb Pathog ; 191: 106678, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38718954

RESUMEN

A conditionally pathogenic bacterium called Bibersteinia trehalosi inhabits the upper respiratory tract of ruminants and is becoming a significant cause of pneumonia, especially in goats. In this study, we identified a gram-negative bacteria strain isolated from dead goat's lungs, which was named M01. By integrating the outcomes of its morphological and biochemical characterization with the investigation of the 16S rRNA gene sequence analysis, the isolate was identified as B. trehalosi. Based on antibiotic susceptibility tests, the isolate was shown to be resistant to ß-lactams, tetracyclines, and amphenicols. Its genome was discovered to comprise 2115 encoded genes and a circular chromosome measuring 2,345,568 bp using whole genome sequencing. Annotation of the VFBD database revealed that isolate M01 had four virulence genes encoding three virulence factors. The CARD database revealed that its genome has two antibiotic-resistance genes. Based on pathogenicity testing, isolate M01 was highly pathogenic to mice, primarily causing pneumonia, with an LD50 of 1.31 × 107 CFU/ml. Moreover, histopathology showed loss of alveolar structure and infiltration of lung inflammatory cells. Hence, the current study could provide sufficient information for prevention and control strategies for future epidemics of B. trehalosi in goat species.


Asunto(s)
Antibacterianos , Genoma Bacteriano , Cabras , Pulmón , Pruebas de Sensibilidad Microbiana , ARN Ribosómico 16S , Factores de Virulencia , Animales , Cabras/microbiología , ARN Ribosómico 16S/genética , Ratones , Antibacterianos/farmacología , Pulmón/microbiología , Pulmón/patología , Factores de Virulencia/genética , Enfermedades de las Cabras/microbiología , Secuenciación Completa del Genoma , Filogenia , Virulencia , Farmacorresistencia Bacteriana , ADN Bacteriano/genética
6.
Chemosphere ; 354: 141677, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38467198

RESUMEN

The bioavailability of contaminants in aquatic environments was highly related with the existing forms (soluble or adsorbed) and properties of dissolved organic matters (DOMs). In this study, the molecular weight (MWs)-dependent effects of DOMs on the adsorption and bioavailability of sulfadiazine were explored. Colloid ZnO and Al2O3 were employed as the representative colloidal particles, and algae-derived organic matter (AOM) and humic acid (HA) were selected as typical autochthonous and allochthonous DOMs. The ultrafiltration procedure was applied to divide the bulk DOMs into high MW (HMW-, 1 kDã0.45 µm) and low MW (LMW-, <1 kDa) fractions. Results showed that HMW-DOM contained more aromatic and protein-like substances as compared to the LMW counterparts. In addition, presence of AOM promoted sulfadiazine adsorption capabilities by 1.19-4.54 folds and mitigated the inhibition ratio by 0.56-0.78 folds, whereas those of HA inhibited sulfadiazine adsorption by 0.27-0.84 folds and enhanced the biotoxicity by 1.21-1.45 folds. Regardless of different DOM types, HMW-fraction exhibited highest effects on sulfadiazine adsorption and bioavailability, followed by the bulk- and LMW-fractions. Two-dimensional correlation spectroscopy showed that sulfadiazine was adsorbed on colloidal surfaces prior to AOM, and the subsequent adsorption of AOM can provide additional sites for sulfadiazine adsorption, which decreased the concentrations of aqueous sulfadiazine as well as the biotoxicity to Microcystis aeruginosa (M. aeruginosa). The HA, however, was preferentially adsorbed on colloidal surfaces, which hindered the subsequent sulfadiazine adsorption and resulted in a high sulfadiazine abundance in aqueous solution as well as the enhanced biotoxicity to M. aeruginosa. This study highlighted the importance of the types and MWs of DOMs in influencing the behaviors and ecological effects of aquatic contaminants.


Asunto(s)
Materia Orgánica Disuelta , Sustancias Húmicas , Peso Molecular , Adsorción , Disponibilidad Biológica , Sustancias Húmicas/análisis
7.
Chemosphere ; 352: 141264, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38244867

RESUMEN

The oxygenation of Fe(II)-bearing minerals for hydroxyl radicals (HO•) formation and contaminant attenuation receives increasing attentions. However, information on dissolved organic matter (DOM) with different types, concentrations, and molecular weights (MWs) in manipulating HO• formation and contaminant attenuation during mineral oxygenation remain unclear. In this study, four iron-pillared montmorillonites (IPMs) and two DOM samples [e.g., humic acids (HA) and fulvic acids (FA)] were prepared to explore the HO• formation and phenanthrene attenuation during the oxygenation of IPMs in the presence or absence of DOMs. Results showed that iron-pillared and high-temperature calcination procedures extended the interlayer domain of IPMs, which provided favorable conditions for a high HO• production from 1293 to 14537 µmol kg-1. The surface-absorbed/low crystalline Fe(Ⅱ) was the predominant Fe(Ⅱ) fractionations for HO• production, and presence of DOMs significantly enhanced the HO• production and phenanthrene attenuation. Moreover, regardless of the types and concentrations, the low MW (LMW, <1 kDa) fraction within DOM pool contributed highest to HO• production and phenanthrene attenuation, followed by the bulk and high MW (HMW-, 1 kDa∼0.45 µm) fractions, and FA exhibited more efficient effects in promoting HO• production and phenanthrene attenuation than HA. The fluorescent spectral analysis further revealed that phenolic-like fluorophores in LMW-fraction were the main substances responsible for the enhanced HO• production and phenanthrene attenuation. The results deepen our understandings toward the behaviors and fate of aquatic HO• and contaminants, and also provide technical guidance for the remediation of contaminated environments.


Asunto(s)
Hierro , Fenantrenos , Hierro/química , Materia Orgánica Disuelta , Radical Hidroxilo/química , Bentonita , Compuestos Ferrosos , Sustancias Húmicas/análisis
8.
Chem Biodivers ; : e202302048, 2024 Jan 23.
Artículo en Inglés | MEDLINE | ID: mdl-38263380

RESUMEN

Today, the bacterial infections caused by multidrug-resistant pathogens seriously threaten human health. Thereby, there is an urgent need to discover antibacterial drugs with novel mechanism. Here, novel psoralen derivatives had been designed and synthesized by a scaffold hopping strategy. Among these targeted twenty-five compounds, compound ZM631 showed the best antibacterial activity against methicillin-resistant S. aureus (MRSA) with the low MIC of 1 µg/mL which is 2-fold more active than that of the positive drug gepotidacin. Molecular docking study revealed that compound ZM631 fitted well in the active pockets of bacterial S. aureus DNA gyrase and formed a key hydrogen bond binding with the residue ASP-1083. These findings demonstrated that the psoralen scaffold could serve as an antibacterial lead compound for further drug development against multidrug-resistant bacterial infections.

9.
J Gen Virol ; 105(1)2024 01.
Artículo en Inglés | MEDLINE | ID: mdl-38270573

RESUMEN

Since the large-scale outbreak of porcine epidemic diarrhoea (PED) in 2010, caused by the genotype 2 (G2) variant of the porcine epidemic diarrhoea virus (PEDV), pig farms in China, even those vaccinated with the G2b vaccine, have experienced infections from the G2a variant, leading to significant economic losses. This study successfully isolated the G2a strain DY2020 from positive small intestine contents (SICs) by blind passage on Vero cells for four generations. The SICs were taken from Daye, Hubei Province, China. The biological characteristics were identified by indirect immunofluorescence assay (IFA) and transmission electron microscopy (TEM). The growth kinetics of the strain on Vero cells were detected by TCID50, and the virus titre could reach 107.35 TCID50 ml-1 (SD: 5.07×106). The pathogenicity towards colostrum-deprived piglets was conducted by assessing faecal viral shedding, morphometric analysis of intestinal lesions, and immunohistochemical staining. The results showed that DY2020 was highly virulent to colostrum-deprived piglets, with severe watery diarrhoea and other clinical symptoms appeared at 6 h post-infection (h p.i.), and all died within 30 h. Pathological tissue examination results showed that the lesions mainly occurred in the intestines of piglets, causing pathological changes such as shortening of intestinal villi. In summary, the discovery of the G2a strain DY2020 in this study is of great significance for understanding Hubei PEDV and provides an important theoretical basis for the development of new efficient PEDV vaccines.


Asunto(s)
Virus de la Diarrea Epidémica Porcina , Chlorocebus aethiops , Animales , Porcinos , Virulencia , Células Vero , China , Diarrea/veterinaria
11.
Clin Colon Rectal Surg ; 36(6): 415-422, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37795471

RESUMEN

Colorectal cancer peritoneal metastases (CRC-PM) are present in 5 to 15% of instances of CRC, and the overall survival (OS) of patients with CRC-PM is much lower than that of patients with other isolated metastatic locations. In recent years, the introduction of cytoreductive surgery (CRS) in conjunction with hyperthermic intraperitoneal chemotherapy has resulted in a significant improvement in CRC-PM patients' OS. Despite this, a significant proportion of CRS patients continue to suffer complications of grades III to V or even die during the perioperative period. Early diagnosis, optimization of patient selection criteria, and refining of individualized combination therapy are necessary for these patients. In this review, we evaluate studies examining the relationship between molecular status and CRS in CRC-PM. Our objective is to gain a comprehensive understanding of how the altered molecular status of CRC-PM impacts CRS, which could increase the likelihood of tailored therapy in the future.

12.
Vaccines (Basel) ; 11(8)2023 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-37631860

RESUMEN

Mycoplasma hyopneumoniae is the etiological agent of porcine enzootic pneumonia (EP), leading to a mild and chronic pneumonia in swine. Relative control has been attained through active vaccination programs, but porcine enzootic pneumonia remains a significant economic challenge in the swine industry. Cellular immunity plays a key role in the prevention and control of porcine enzootic pneumonia. Therefore, the development of a more efficient vaccine that confers a strong immunity against M. hyopneumoniae is necessary. In this study, a multi-antigen chimera (L9m6) was constructed by combining the heat-labile enterotoxin B subunit (LTB) with three antigens of M. hyopneumoniae (P97R1, mhp390, and P46), and its immunogenic and antigenic properties were assessed in a murine model. In addition, we compared the effect of individual administration and multiple-fusion of these antigens. The chimeric multi-fusion vaccine induced significant cellular immune responses and high production of IgG and IgM antibodies against M. hyopneumoniae. Collectively, our data suggested that rL9m6 chimera exhibits potential as a viable vaccine candidate for the prevention and control of porcine enzootic pneumonia.

13.
Int J Mol Sci ; 24(14)2023 Jul 24.
Artículo en Inglés | MEDLINE | ID: mdl-37511601

RESUMEN

Actinobacillus pleuropneumoniae (APP) is the causative pathogen of porcine pleuropneumonia, a highly contagious respiratory disease in the pig industry. The increasingly severe antimicrobial resistance in APP urgently requires novel antibacterial alternatives for the treatment of APP infection. In this study, we investigated the effect of tea polyphenols (TP) against APP. MIC and MBC of TP showed significant inhibitory effects on bacteria growth and caused cellular damage to APP. Furthermore, TP decreased adherent activity of APP to the newborn pig tracheal epithelial cells (NPTr) and the destruction of the tight adherence junction proteins ß-catenin and occludin. Moreover, TP improved the survival rate of APP infected mice but also attenuated the release of the inflammation-related cytokines IL-6, IL-8, and TNF-α. TP inhibited activation of the TLR/MAPK/PKC-MLCK signaling for down-regulated TLR-2, TLR4, p-JNK, p-p38, p-PKC-α, and MLCK in cells triggered by APP. Collectively, our data suggest that TP represents a promising therapeutic agent in the treatment of APP infection.


Asunto(s)
Infecciones por Actinobacillus , Actinobacillus pleuropneumoniae , Actinobacillus , Infecciones por Mycoplasma , Pleuroneumonía , Enfermedades de los Porcinos , Animales , Porcinos , Ratones , Pleuroneumonía/microbiología , Receptor Toll-Like 4/metabolismo , Uniones Estrechas , Pulmón/microbiología , Infecciones por Actinobacillus/tratamiento farmacológico , Infecciones por Actinobacillus/microbiología , Té/metabolismo , Enfermedades de los Porcinos/microbiología
14.
Front Genet ; 14: 1211020, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37351347

RESUMEN

Introduction: Outer membrane proteins are crucial in maintaining the structural stability and permeability of the outer membrane. Outer membrane proteins exhibit several functions such as antigenicity and strong immunogenicity, which have potential applications in clinical diagnosis and disease prevention. However, wet experiments for studying OMPs are time and capital-intensive, thereby necessitating the use of computational methods for their identification. Methods: In this study, we developed a computational model to predict outer membrane proteins. The non-redundant dataset consists of a positive set of 208 outer membrane proteins and a negative set of 876 non-outer membrane proteins. In this study, we employed the pseudo amino acid composition method to extract feature vectors and subsequently utilized the support vector machine for prediction. Results and Discussion: In the Jackknife cross-validation, the overall accuracy and the area under receiver operating characteristic curve were observed to be 93.19% and 0.966, respectively. These results demonstrate that our model can produce accurate predictions, and could serve as a valuable guide for experimental research on outer membrane proteins.

15.
Microbiol Spectr ; 11(3): e0433722, 2023 06 15.
Artículo en Inglés | MEDLINE | ID: mdl-37212676

RESUMEN

Streptococcus suis is an recognized zoonotic pathogen of swine and severely threatens human health. Zinc is the second most abundant transition metal in biological systems. Here, we investigated the contribution of zinc to the drug resistance and pathogenesis of S. suis. We knocked out the genes of AdcACB and Lmb, two Zn-binding lipoproteins. Compared to the wild-type strain, we found that the survival rate of this double-mutant strain (ΔadcAΔlmb) was reduced in Zinc-limited medium, but not in Zinc-supplemented medium. Additionally, phenotypic experiments showed that the ΔadcAΔlmb strain displayed impaired adhesion to and invasion of cells, biofilm formation, and tolerance of cell envelope-targeting antibiotics. In a murine infection model, deletion of the adcA and lmb genes in S. suis resulted in a significant decrease in strain virulence, including survival rate, tissue bacterial load, inflammatory cytokine levels, and histopathological damage. These findings show that AdcA and Lmb are important for biofilm formation, drug resistance, and virulence in S. suis. IMPORTANCE Transition metals are important micronutrients for bacterial growth. Zn is necessary for the catalytic activity and structural integrity of various metalloproteins involved in bacterial pathogenic processes. However, how these invaders adapt to host-imposed metal starvation and overcome nutritional immunity remains unknown. Thus, pathogenic bacteria must acquire Zn during infection in order to successfully survive and multiply. The host uses nutritional immunity to limit the uptake of Zn by the invading bacteria. The bacterium uses a set of high-affinity Zn uptake systems to overcome this host metal restriction. Here, we identified two Zn uptake transporters in S. suis, AdcA and Lmb, by bioinformatics analysis and found that an adcA and lmb double-mutant strain could not grow in Zn-deficient medium and was more sensitive to cell envelope-targeting antibiotics. It is worth noting that the Zn uptake system is essential for biofilm formation, drug resistance, and virulence in S. suis. The Zn uptake system is expected to be a target for the development of novel antimicrobial therapies.


Asunto(s)
Proteínas Bacterianas , Streptococcus suis , Animales , Humanos , Ratones , Proteínas Bacterianas/genética , Resistencia a Medicamentos , Streptococcus suis/genética , Porcinos , Virulencia/genética , Zinc
16.
Front Microbiol ; 14: 1200678, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37250059

RESUMEN

Promoters are the basic functional cis-elements to which RNA polymerase binds to initiate the process of gene transcription. Comprehensive understanding gene expression and regulation depends on the precise identification of promoters, as they are the most important component of gene expression. This study aimed to develop a machine learning-based model to predict promoters in Klebsiella aerogenes (K. aerogenes). In the prediction model, the promoter sequences in K. aerogenes genome were encoded by pseudo k-tuple nucleotide composition (PseKNC) and position-correlation scoring function (PCSF). Numerical features were obtained and then optimized using mRMR by combining with support vector machine (SVM) and 5-fold cross-validation (CV). Subsequently, these optimized features were inputted into SVM-based classifier to discriminate promoter sequences from non-promoter sequences in K. aerogenes. Results of 10-fold CV showed that the model could yield the overall accuracy of 96.0% and the area under the ROC curve (AUC) of 0.990. We hope that this model will provide help for the study of promoter and gene regulation in K. aerogenes.

17.
Int J Mol Sci ; 24(8)2023 Apr 18.
Artículo en Inglés | MEDLINE | ID: mdl-37108608

RESUMEN

Streptococcus suis (S. suis) is one of the most important zoonotic pathogens that threaten the lives of pigs and humans. Even worse, the increasingly severe antimicrobial resistance in S. suis is becoming a global issue. Therefore, there is an urgent need to discover novel antibacterial alternatives for the treatment of S. suis infection. In this study, we investigated theaflavin (TF1), a benzoaphenone compound extracted from black tea, as a potential phytochemical compound against S. suis. TF1 at MIC showed significant inhibitory effects on S. suis growth, hemolytic activity, and biofilm formation, and caused damage to S. suis cells in vitro. TF1 had no cytotoxicity and decreased adherent activity of S. suis to the epithelial cell Nptr. Furthermore, TF1 not only improved the survival rate of S. suis-infected mice but also reduced the bacterial load and the production of IL-6 and TNF-α. A hemolysis test revealed the direct interaction between TF1 and Sly, while molecular docking showed TF1 had a good binding activity with the Glu198, Lys190, Asp111, and Ser374 of Sly. Moreover, virulence-related genes were downregulated in the TF1-treated group. Collectively, our findings suggested that TF1 can be used as a potential inhibitor for treating S. suis infection in view of its antibacterial and antihemolytic activity.


Asunto(s)
Biflavonoides , Infecciones Estreptocócicas , Streptococcus suis , Humanos , Animales , Porcinos , Ratones , Simulación del Acoplamiento Molecular , Biflavonoides/farmacología , Biflavonoides/uso terapéutico , Infecciones Estreptocócicas/tratamiento farmacológico , Infecciones Estreptocócicas/microbiología , Antibacterianos/uso terapéutico , Proteínas Hemolisinas/metabolismo
18.
Front Genet ; 14: 1157021, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36926588

RESUMEN

Introduction: Apoptosis proteins play an important role in the process of cell apoptosis, which makes the rate of cell proliferation and death reach a relative balance. The function of apoptosis protein is closely related to its subcellular location, it is of great significance to study the subcellular locations of apoptosis proteins. Many efforts in bioinformatics research have been aimed at predicting their subcellular location. However, the subcellular localization of apoptotic proteins needs to be carefully studied. Methods: In this paper, based on amphiphilic pseudo amino acid composition and support vector machine algorithm, a new method was proposed for the prediction of apoptosis proteins\x{2019} subcellular location. Results and Discussion: The method achieved good performance on three data sets. The Jackknife test accuracy of the three data sets reached 90.5%, 93.9% and 84.0%, respectively. Compared with previous methods, the prediction accuracies of APACC_SVM were improved.

19.
Sci Total Environ ; 870: 161870, 2023 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-36731571

RESUMEN

The heavy metal Cd can cause severe toxicity on aquatic algae, but there are few studies on the cytotoxicity of heavy metal on algae based on synchrotron radiation technology. In this study, synchrotron radiation-based Fourier transform infrared spectromicroscopy (SR-FTIR) was used to characterize in vivo the toxic effects of Cd on Cosmarium sp. cells, emphasizing the influence of dissolved organic matter (DOM) on Cd toxicity. Results showed that, in the absence of DOM, obvious growth inhibition, cell volume reduction, and photosynthesis disruption could be observed with increasing Cd concentrations (0-500 µg/L). Based on the SR-FTIR imaging and functional group quantification, it was shown that the biosynthesis of biomolecules such as proteins, lipids, and carbohydrates was inhibited in algal cells. However, the addition of DOM caused significant heterogeneities in biomacromolecule biosynthesis that an increased biosynthesis of carbohydrates and structural lipids but an inhibited biosynthesis of proteins and storage lipids were observed. Furthermore, the correlation analysis and principal component analysis showed a good correlation between v(C-OH)/Amide II and biochemical parameters, indicating that changes of carbohydrates could be used as the biomarker to indicate the cytotoxicity of heavy metals to algal cells. These findings provide insight into the mechanisms of heavy metal cytotoxicity to aquatic algae and systematic cytotoxicity assessment under various aquatic conditions.


Asunto(s)
Chlorophyta , Metales Pesados , Cadmio/análisis , Materia Orgánica Disuelta , Espectroscopía Infrarroja por Transformada de Fourier/métodos , Sincrotrones , Chlorophyta/metabolismo , Plantas/metabolismo , Carbohidratos , Lípidos
20.
Viruses ; 15(2)2023 02 14.
Artículo en Inglés | MEDLINE | ID: mdl-36851748

RESUMEN

Japanese encephalitis virus (JEV) infection causes host endoplasmic reticulum stress (ERS) reaction, and then induces cell apoptosis through the UPR pathway, invading the central nervous system and causing an inflammation storm. The endoplasmic reticulum stress inhibitor, 4-phenyl-butyric acid (4-PBA), has an inhibitory effect on the replication of flavivirus. Here, we studied the effect of 4-PBA on JEV infection both in vitro and vivo. The results showed that 4-PBA treatment could significantly decrease the titer of JEV, inhibit the expression of the JEV NS3 protein (in vitro, p < 0.01) and reduce the positive rate of the JEV E protein (in vivo, p < 0.001). Compared to the control group, 4-PBA treatment can restore the weight of JEV-infected mice, decrease the level of IL-1ß in serum and alleviate the abnormalities in brain tissue structure. Endoplasmic reticulum stress test found that the expression level of GRP78 was much lower and activation levels of PERK and IRE1 pathways were reduced in the 4-PBA treatment group. Furthermore, 4-PBA inhibited the UPR pathway activated by NS3, NS4b and NS5 RdRp. The above results indicated that 4-PBA could block JEV replication and inhibit ER stress caused by JEV. Interestingly, 4-PBA could reduce the expression of NS5 by inhibiting transcription (p < 0.001), but had no effect on the expression of NS3 and NS4b. This result may indicate that 4-PBA has antiviral activity independent of the UPR pathway. In summary, the effect of 4-PBA on JEV infection is related to the inhibition of ER stress, and it may be a promising drug for the treatment of Japanese encephalitis.


Asunto(s)
Virus de la Encefalitis Japonesa (Especie) , Virus de la Encefalitis Japonesa (Subgrupo) , Encefalitis Japonesa , Animales , Ratones , Ácido Butírico , Encefalitis Japonesa/tratamiento farmacológico , Estrés del Retículo Endoplásmico
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