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1.
Nucleic Acids Res ; 2024 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-39271121

RESUMO

MicroRNAs (miRNAs) are short non-coding RNAs involved in various cellular processes, playing a crucial role in gene regulation. Identifying miRNA targets remains a central challenge and is pivotal for elucidating the complex gene regulatory networks. Traditional computational approaches have predominantly focused on identifying miRNA targets through perfect Watson-Crick base pairings within the seed region, referred to as canonical sites. However, emerging evidence suggests that perfect seed matches are not a prerequisite for miRNA-mediated regulation, underscoring the importance of also recognizing imperfect, or non-canonical, sites. To address this challenge, we propose Mimosa, a new computational approach that employs the Transformer framework to enhance the prediction of miRNA targets. Mimosa distinguishes itself by integrating contextual, positional and base-pairing information to capture in-depth attributes, thereby improving its predictive capabilities. Its unique ability to identify non-canonical base-pairing patterns makes Mimosa a standout model, reducing the reliance on pre-selecting candidate targets. Mimosa achieves superior performance in gene-level predictions and also shows impressive performance in site-level predictions across various non-human species through extensive benchmarking tests. To facilitate research efforts in miRNA targeting, we have developed an easy-to-use web server for comprehensive end-to-end predictions, which is publicly available at http://monash.bioweb.cloud.edu.au/Mimosa.

2.
Brief Bioinform ; 24(6)2023 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-37950905

RESUMO

Cancer genomics is dedicated to elucidating the genes and pathways that contribute to cancer progression and development. Identifying cancer genes (CGs) associated with the initiation and progression of cancer is critical for characterization of molecular-level mechanism in cancer research. In recent years, the growing availability of high-throughput molecular data and advancements in deep learning technologies has enabled the modelling of complex interactions and topological information within genomic data. Nevertheless, because of the limited labelled data, pinpointing CGs from a multitude of potential mutations remains an exceptionally challenging task. To address this, we propose a novel deep learning framework, termed self-supervised masked graph learning (SMG), which comprises SMG reconstruction (pretext task) and task-specific fine-tuning (downstream task). In the pretext task, the nodes of multi-omic featured protein-protein interaction (PPI) networks are randomly substituted with a defined mask token. The PPI networks are then reconstructed using the graph neural network (GNN)-based autoencoder, which explores the node correlations in a self-prediction manner. In the downstream tasks, the pre-trained GNN encoder embeds the input networks into feature graphs, whereas a task-specific layer proceeds with the final prediction. To assess the performance of the proposed SMG method, benchmarking experiments are performed on three node-level tasks (identification of CGs, essential genes and healthy driver genes) and one graph-level task (identification of disease subnetwork) across eight PPI networks. Benchmarking experiments and performance comparison with existing state-of-the-art methods demonstrate the superiority of SMG on multi-omic feature engineering.


Assuntos
Neoplasias , Oncogenes , Mutação , Benchmarking , Genes Essenciais , Genômica , Neoplasias/genética
3.
Brief Bioinform ; 23(6)2022 11 19.
Artigo em Inglês | MEDLINE | ID: mdl-36341591

RESUMO

Subcellular localization of messenger RNAs (mRNAs) plays a key role in the spatial regulation of gene activity. The functions of mRNAs have been shown to be closely linked with their localizations. As such, understanding of the subcellular localizations of mRNAs can help elucidate gene regulatory networks. Despite several computational methods that have been developed to predict mRNA localizations within cells, there is still much room for improvement in predictive performance, especially for the multiple-location prediction. In this study, we proposed a novel multi-label multi-class predictor, termed Clarion, for mRNA subcellular localization prediction. Clarion was developed based on a manually curated benchmark dataset and leveraged the weighted series method for multi-label transformation. Extensive benchmarking tests demonstrated Clarion achieved competitive predictive performance and the weighted series method plays a crucial role in securing superior performance of Clarion. In addition, the independent test results indicate that Clarion outperformed the state-of-the-art methods and can secure accuracy of 81.47, 91.29, 79.77, 92.10, 89.15, 83.74, 80.74, 79.23 and 84.74% for chromatin, cytoplasm, cytosol, exosome, membrane, nucleolus, nucleoplasm, nucleus and ribosome, respectively. The webserver and local stand-alone tool of Clarion is freely available at http://monash.bioweb.cloud.edu.au/Clarion/.


Assuntos
Núcleo Celular , Proteínas , RNA Mensageiro/genética , Núcleo Celular/genética , Biologia Computacional/métodos , Bases de Dados de Proteínas
4.
Bioinformatics ; 39(3)2023 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-36864612

RESUMO

MOTIVATION: Multiple instance learning (MIL) is a powerful technique to classify whole slide images (WSIs) for diagnostic pathology. The key challenge of MIL on WSI classification is to discover the critical instances that trigger the bag label. However, tumor heterogeneity significantly hinders the algorithm's performance. RESULTS: Here, we propose a novel multiplex-detection-based multiple instance learning (MDMIL) which targets tumor heterogeneity by multiplex detection strategy and feature constraints among samples. Specifically, the internal query generated after the probability distribution analysis and the variational query optimized throughout the training process are utilized to detect potential instances in the form of internal and external assistance, respectively. The multiplex detection strategy significantly improves the instance-mining capacity of the deep neural network. Meanwhile, a memory-based contrastive loss is proposed to reach consistency on various phenotypes in the feature space. The novel network and loss function jointly achieve high robustness towards tumor heterogeneity. We conduct experiments on three computational pathology datasets, e.g. CAMELYON16, TCGA-NSCLC, and TCGA-RCC. Benchmarking experiments on the three datasets illustrate that our proposed MDMIL approach achieves superior performance over several existing state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION: MDMIL is available for academic purposes at https://github.com/ZacharyWang-007/MDMIL.


Assuntos
Carcinoma Pulmonar de Células não Pequenas , Neoplasias Pulmonares , Humanos , Benchmarking , Redes Neurais de Computação , Fenótipo
5.
Bioinformatics ; 39(3)2023 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-36794913

RESUMO

MOTIVATION: The rapid accumulation of high-throughput sequence data demands the development of effective and efficient data-driven computational methods to functionally annotate proteins. However, most current approaches used for functional annotation simply focus on the use of protein-level information but ignore inter-relationships among annotations. RESULTS: Here, we established PFresGO, an attention-based deep-learning approach that incorporates hierarchical structures in Gene Ontology (GO) graphs and advances in natural language processing algorithms for the functional annotation of proteins. PFresGO employs a self-attention operation to capture the inter-relationships of GO terms, updates its embedding accordingly and uses a cross-attention operation to project protein representations and GO embedding into a common latent space to identify global protein sequence patterns and local functional residues. We demonstrate that PFresGO consistently achieves superior performance across GO categories when compared with 'state-of-the-art' methods. Importantly, we show that PFresGO can identify functionally important residues in protein sequences by assessing the distribution of attention weightings. PFresGO should serve as an effective tool for the accurate functional annotation of proteins and functional domains within proteins. AVAILABILITY AND IMPLEMENTATION: PFresGO is available for academic purposes at https://github.com/BioColLab/PFresGO. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Aprendizado Profundo , Anotação de Sequência Molecular , Ontologia Genética , Biologia Computacional/métodos , Algoritmos , Proteínas/metabolismo
6.
Crit Rev Food Sci Nutr ; : 1-20, 2024 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-38189263

RESUMO

Tryptophan (TRP) contributes to individual immune homeostasis and good condition via three complex metabolism pathways (5-hydroxytryptamine (5-HT), kynurenine (KP), and gut microbiota pathway). Indole propionic acid (IPA), one of the TRP derivatives of the microbiota pathway, has raised more attention because of its impact on metabolic disorders. Here, we retrospect increasing evidence that TRP metabolites/IPA derived from its proteolysis impact host health and disease. IPA can activate the immune system through aryl hydrocarbon receptor (AHR) and/or Pregnane X receptor (PXR) as a vital mediator among diet-caused host and microbe cross-talk. Different levels of IPA in systemic circulation can predict the risk of NAFLD, T2DM, and CVD. IPA is suggested to alleviate cognitive impairment from oxidative damage, reduce gut inflammation, inhibit lipid accumulation and attenuate the symptoms of NAFLD, putatively enhance the intestinal epithelial barrier, and maintain intestinal homeostasis. Now, we provide a general description of the relationships between IPA and various physiological and pathological processes, which support an opportunity for diet intervention for metabolic diseases.

7.
Pacing Clin Electrophysiol ; 47(8): 1025-1031, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38881174

RESUMO

BACKGROUND: An accurate display of scar-related atrial tachycardia (ATs) is a key determinant of ablation success. The efficacy of ripple mapping (RM) in identifying the mechanism and critical isthmus of scar-related ATs during coherent mapping is unknown. METHODS: A total of 97 patients with complex ATs who underwent radiofrequency catheter ablation at our center between October 2018 and September 2022 were included. ATs was mapped using a multielectrode mapping catheter on the CARTO3v7 CONFIDENCE module. Coherent and RM were used to identify the reentrant circuit. RESULTS: The mechanisms of 128 ATs were analyzed retrospectively (84 anatomic-reentrant ATs and 44 non-anatomic reentrant ATs). The median AT cycle length was 264 ± 25ms. The correct diagnosis was achieved in 83 ATs (68%) using only coherent mapping. Through coherent mapping plus RM, 114 ATs (84.2%) were correctly diagnosed (68% vs. 89%, p = .019). In non-anatomical reentrant ATs, 81% of the diagnostic rate was achieved by reviewing both coherent and ripple mapping compared to reviewing coherent mapping alone (81% vs. 52%, p = .03). Reviewing coherent mapping and ripple mapping showed a higher diagnostic rate in patients who underwent cardiac surgery than those with Coherent mapping alone (64% vs. 88%, p = .04). CONCLUSION: Coherent mapping combined with RM was superior to coherent mapping alone in identifying the mechanism of scar-related ATs post-cardiac surgery and non-anatomic reentrant ATs.


Assuntos
Ablação por Cateter , Cicatriz , Humanos , Cicatriz/fisiopatologia , Masculino , Feminino , Ablação por Cateter/métodos , Estudos Retrospectivos , Pessoa de Meia-Idade , Taquicardia Supraventricular/cirurgia , Taquicardia Supraventricular/fisiopatologia , Técnicas Eletrofisiológicas Cardíacas , Idoso
8.
J Enzyme Inhib Med Chem ; 39(1): 2390909, 2024 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-39206852

RESUMO

An oxidising and substituting one-pot reaction strategy has been developed to synthesise dihydromyricetin derivatives with the aim of enhancing the inhibitory activity of dihydromyricetin against SARS-CoV-2. Different ω-methoxy-ω-oxeylkyl was introduced in C7-OH site and yielded eight analogs, all of them showed good inhibitory activity against SARS-CoV-2 3CLpro with IC50 values ranging from 0.72 to 2.36 µM. In the Vero E6-cell, compound 3 has a good activity of anti-SARS-CoV-2 virus (Omicron virus BA.5) in the prevention model, with an EC50 of 15.84 µM, and so do compound 10 in the therapeutic model, with an EC50 of 11.52 µM. The results suggest that the introduction of long chain ω-oxeylkyl at C7-OH facilitate the inhibition of viral replication in the therapeutic model, which is consistent with the binding energies predicted from molecular docking conclusions. It implies that dihydromyricetin derivatives have the potential to become effective inhibitors of SARS-CoV-2 Omicron and other viruses.


Assuntos
Antivirais , Desenho de Fármacos , Flavonóis , SARS-CoV-2 , Antivirais/farmacologia , Antivirais/síntese química , Antivirais/química , Chlorocebus aethiops , SARS-CoV-2/efeitos dos fármacos , Células Vero , Flavonóis/farmacologia , Flavonóis/síntese química , Flavonóis/química , Animais , Relação Estrutura-Atividade , Simulação de Acoplamento Molecular , Replicação Viral/efeitos dos fármacos , Estrutura Molecular , Relação Dose-Resposta a Droga , Testes de Sensibilidade Microbiana , Proteases 3C de Coronavírus/antagonistas & inibidores , Proteases 3C de Coronavírus/metabolismo , Humanos
9.
Dev Genes Evol ; 233(1): 49-57, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36658408

RESUMO

Cold-inducible RNA-binding protein (CIRBP) responds to a wide array of cellular stresses such as cold shock, hypoxia, and inflammatory responses. However, functional studies of CIRBP in jawless vertebrates are limited. In this study, a CIRBP homolog from the jawless vertebrate lamprey (Lethenteron reissneri) was cloned and characterized (named Lr-CIRBP). The cDNA fragment of Lr-CIRBP has a 516 bp open reading frame (ORF) that encodes 171 amino acids, comprising a glycine-rich region at the C-terminal, similar to higher vertebrates but slightly shorter, and an RNA recognition motif (RRM) domain at the N-terminus. The predicted Lr-CIRBP sequence had 51.4 ~ 70.6% similarity with CIRBPs from other vertebrates. Further phylogenetic analysis revealed that Lr-CIRBP is located in the outgroup of vertebrates and is the ancestor of vertebrates. Based on real-time quantitative PCR experimental analysis, Lr-CIRBP expression was highest in leukocytes and increased significantly after multi-stimulation, peaking at 12 h. RNA interference showed that Lr-CIRBP knockdown can down-regulate the expression of inflammatory factors in Lethenteron reissneri. In conclusion, our study successfully clarifies the ancestral features and functions of CIRBP, while revealing valuable insight into how the protein is involved in the immune responses of a jawless vertebrate.


Assuntos
Lampreias , Proteínas de Ligação a RNA , Animais , Lampreias/genética , Filogenia , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo
10.
J Org Chem ; 88(11): 7564-7570, 2023 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-37137822

RESUMO

Allylic C-H cyclopropanation of α-methylstyrene and its derivatives was realized through a one-pot two-step sequence, formally converting two aliphatic C-H bonds to C-C bonds with a good yield and high diastereoselectivity, thus providing a quick entry to the synthetically useful vinyl cyclopropane structures.

11.
BMC Cardiovasc Disord ; 23(1): 612, 2023 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-38093240

RESUMO

BACKGROUND: There are sex differences in many risk factors associated with coronary artery disease (CAD). CT-derived fractional flow reserve (CT-FFR) and fat attenuation index (FAI) have been shown to independently predict cardiovascular events. We aimed to examine the impact of sex on the prognostic value of CT-FFR and FAI in suspected CAD patients, and to examine the incremental prognostic value of FAI over CT-FFR in both sex. METHODS: A total of 1334 consecutive suspected CAD subjects who underwent coronary computed tomographic angiography (CCTA) were retrospectively collected. We divided the patients into males and females and calculated CT-FFR and FAI data from CCTA images. Kaplan-Meier analysis was used to assess the risk of major adverse cardiovascular events (MACE) stratified by CT-FFR and FAI in both sex. Cox regression models were used to assess the incremental prognostic value of FAI by adding the variable to a model that included CT-FFR and clinical variables. RESULTS: During a median follow-up of 2.08 years, 212 patients had MACE. CT-FFR ≤ 0.80 was significantly associated with MACE in both sex. FAI value of left anterior descending artery (FAI[LAD]) and FAI value of left circumflex (FAI[LCX]) ≥ 70.1 were significantly associated with MACE in females. FAI[LCX] added incremental prognostic value over clinical and CT-FFR variables in females, with hazard ratio (HR) 3.230 (1.982-5.265, P = 0.000), Harrel's C 0.669 (P < 0.001), net reclassification improvement (NRI) 0.161 (0.073-0.260, P < 0.001), and integrated discrimination index (IDI) 0.036 (0.008-0.090, P = 0.010). FAI[LAD] did not enhance risk prediction in females (Harrel's C 0.643, P = 0.054; NRI 0.041, P = 0.189; IDI 0.005, P = 0.259). The decision curve analysis demonstrated that the model including FAI[LCX] resulted in the highest net benefit. CONCLUSIONS: In suspected CAD patients, the prognostic value of CT-FFR is not significantly biased by sex. The prognostic value of FAI[LAD] and FAI[LCX] were significantly associated with MACE in females, but not males. FAI[LCX], not FAI[LAD], added incremental prognostic value over CT-FFR and might enhance CT-FFR risk stratification in females.


Assuntos
Doença da Artéria Coronariana , Estenose Coronária , Reserva Fracionada de Fluxo Miocárdico , Humanos , Masculino , Feminino , Doença da Artéria Coronariana/diagnóstico por imagem , Angiografia Coronária/métodos , Estudos Retrospectivos , Prognóstico , Tomografia Computadorizada por Raios X , Angiografia por Tomografia Computadorizada/métodos , Valor Preditivo dos Testes
12.
Int J Mol Sci ; 23(14)2022 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-35887083

RESUMO

Gut bacteria are closely associated with the development of atopic dermatitis (AD) due to their immunoregulatory function. Indole derivatives, produced by gut bacteria metabolizing tryptophan, are ligands to activate the aryl hydrocarbon receptor (AHR), which plays a critical role in attenuating AD symptoms. Limosilactobacillus reuteri, a producer of indole derivatives, regulates mucosal immunity via activating the AHR signaling pathway. However, the effective substance and mechanism of L. reuteri in the amelioration of AD remain to be elucidated. In this research, we found that L. reuteri DYNDL22M62 significantly improved AD-like symptoms in mice by suppressing IgE levels and the expressions of thymic stromal lymphopoietin (TSLP), IL-4, and IL-5. L. reuteri DYNDL22M62 induced an increase in the production of indole lactic acid (ILA) and indole propionic acid (IPA) via targeted tryptophan metabolic analysis and the expression of AHR in mice. Furthermore, L. reuteri DYNDL22M62 increased the proportions of Romboutsia and Ruminococcaceae NK4A214 group, which were positively related to ILA, but decreased Dubosiella, which was negatively related to IPA. Collectively, L. reuteri DYNDL22M62 with the role of modulating gut bacteria and the production of indole derivatives may attenuate AD via activating AHR in mice.


Assuntos
Dermatite Atópica , Limosilactobacillus reuteri , Animais , Bactérias/metabolismo , Dermatite Atópica/metabolismo , Indóis/metabolismo , Indóis/farmacologia , Limosilactobacillus reuteri/metabolismo , Camundongos , Receptores de Hidrocarboneto Arílico/genética , Receptores de Hidrocarboneto Arílico/metabolismo , Triptofano/metabolismo
13.
Acta Radiol ; 62(3): 414-422, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32571098

RESUMO

BACKGROUND: We know little about the changes of brain activity in patients with normal-tension glaucoma (NTG). PURPOSE: To investigate the altered spontaneous brain activity in patients with NTG through the resting state functional magnetic resonance imaging-fractional amplitude of low-frequency fluctuation (rsfMRI-fALFF) technique, and to explore the relationship with optical coherence tomography (OCT) and field of vision. MATERIAL AND METHODS: Twenty patients with NTG and 20 healthy controls (HCs) (matched for sex, age, and level of education) were enrolled. Spontaneous cerebral activity variations were investigated using the rsfMRI-fALFF technique in all individuals. The average fALFF values of patients with NTG and HCs were compared. RESULTS: Compared with HCs, patients with NTG had significantly lower fALFF values in the right angular gyrus and precuneus; however, higher fALFF values in the brain regions were not observed. The values showed statistically significant negative correlation with those of the retinal nerve fiber layer (right angular gyrus: r = -0.607, P = 0.010; right precuneus: r = -0.504, P = 0.020). There was no significant correlation between the fALFF value and cup-disc ratio (right angular gyrus: r = 0.158, P = 0.494; right precuneus: r = -0.087, P = 0.706), mean deviation (right angular gyrus: r = 0.096, P = 0.468; right precuneus: r = 0.026, P = 0.845), and pattern SD value (right angular gyrus: r = 0.064, P = 0.626; right precuneus: r = -0.145, P = 0.268). CONCLUSION: Abnormal spontaneous activities were detected in numerous brain regions of patients with NTG, which may provide useful information for understanding the dysfunction in NTG. These activity changes in brain regions may be used as effective clinical indicators for NTG.


Assuntos
Glaucoma de Baixa Tensão/diagnóstico por imagem , Glaucoma de Baixa Tensão/fisiopatologia , Formação Reticular Mesencefálica/fisiopatologia , Lobo Parietal/fisiopatologia , Campos Visuais/fisiologia , Adulto , Idoso , Mapeamento Encefálico , Estudos de Casos e Controles , Feminino , Humanos , Imageamento por Ressonância Magnética , Masculino , Formação Reticular Mesencefálica/diagnóstico por imagem , Pessoa de Meia-Idade , Lobo Parietal/diagnóstico por imagem , Tomografia de Coerência Óptica
14.
Microb Pathog ; 147: 104292, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32505653

RESUMO

BACKGROUND AND AIMS: Helicobacter pylori (H. pylori) infection can occur in early childhood, without eradication therapies such infection can persist throughout life and cause many different diseases. This study investigated the metabolic characteristics and explored the underlying mechanism of children with H. pylori infection, and identified potential biomarkers for evaluating the efficacy of H. pylori eradication therapies. METHODS: We performed 1H NMR-based metabonomics coupled with multivariate analysis to investigate the metabolic profiling of serum samples between Children with and without H. pylori infection. In the same manner, we compared the alternations of metabolites in H. pylori-infected children before and after H. pylori eradication therapies. RESULTS: 21 metabolites from serum in H. pylori-infected and H. pylori-uninfected children were identified, which were mainly involved in energy, amino acid, lipid and microbial metabolism. We found that the serum levels of trimethylamine N-oxide and alanine were significantly higher in H. pylori-infected children compared to uninfected sera, whereas lactate was significantly lower. We also found that the levels of trimethylamine N-oxide and creatine in H. pylori-infected children was significantly decreased after H. pylori eradication therapies, whereas lactate and low-density lipoprotein/very low-density lipoprotein was significantly increased. CONCLUSIONS: This is the first study using 1H NMR-based metabolomics approach to explore the effects of H. pylori infection in children. Our results demonstrated that the disturbances of metabolism in energy, amino acids, lipids and microbiota could play an important role in the pathogenesis of gastrointestinal and extragastric diseases caused by H. pylori infection. Trimethylamine N-oxide and lactate might serve as potential serum biomarkers for evaluating the efficacy of H. pylori eradication therapies.


Assuntos
Infecções por Helicobacter , Helicobacter pylori , Microbiota , Criança , Pré-Escolar , Humanos , Metabolômica , Espectroscopia de Prótons por Ressonância Magnética
15.
Int J Syst Evol Microbiol ; 67(11): 4449-4455, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-28920837

RESUMO

A novel Gram-stain-positive, motile, endospore-forming, rod-shaped bacterial strain, NEAU-cbsb5T, was isolated from forest soil from Changbai Mountain, Heilongjiang Province, China. The isolate grew at 15-40 °C (optimum 30 °C), at pH 6.0-8.0 (optimum pH 7.0) and in the presence of up to 4 % (w/v) NaCl, although NaCl was not required for growth. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NEAU-cbsb5T formed a distinct lineage within the genus Bacillus and was most closely related to Bacillus acidiceler DSM 18954T (99.1 % similarity) and Bacillus luciferensis JCM 12212T (99.0 %). 16S rRNA gene sequence similarity to sequences of the type strains of other Bacillus species was less than 96.0 %. Average nucleotide identity (ANI) values between NEAU-cbsb5T and its most closely related species were 78.72-84.75 % by ANIm, ANIb and OrthoANIu analysis. The in silico DNA-DNA hybridization values between strain NEAU-cbsb5T and its close relatives B. acidiceler DSM 18954T and B. luciferensis JCM 12212T were both 23.80 %, again indicating they belong to different taxa. The major cellular fatty acids of NEAU-cbsb5T were iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unknown aminophospholipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the predominant menaquinones were MK-7 and MK-6. The genomic DNA G+C content was 33.0 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain NEAU-cbsb5T was classified as a representative of a novel species in the genus Bacillus, for which the name Bacillus solisilvae sp. nov. is proposed. The type strain is NEAU-cbsb5T (=CGMCC 1.14993T=DSM 100485T).


Assuntos
Bacillus/classificação , Florestas , Filogenia , Microbiologia do Solo , Bacillus/genética , Bacillus/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
16.
Surg Radiol Anat ; 39(4): 383-391, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-27717980

RESUMO

PURPOSE: To quantitatively measure the morphology parameters of the right auricle with 256-slice multidetector computed tomography angiography (MDCTA) in healthy people. MATERIALS AND METHODS: A retrospective analysis of 200 patients who had undergone coronary MDCTA with negative findings was performed. The raw imaging data were reconstructed and the right auricular volume, right atrial volume, right auricle height, base long and short axes, base perimeter and area, normal angle, and distance were quantitatively measured. RESULTS: Men had significantly (P < 0.05) greater values than women in the right auricular volume (13.3 ± 4.0 vs. 11.7 ± 3.7 mL) and height (33.0 ± 5.0 vs. 30.5 ± 5.2 mm), the base long axis (34.4 ± 4.1 vs. 33.2 ± 3.9 mm), area (787.6 ± 177.6 vs. 771.0 ± 143.2 mm2) and perimeter (119.2 ± 17.5 vs. 115.0 ± 13.0), and the normal distance (22.4 ± 6.6 vs. 20.2 ± 6.7 mm). The normal 95 % reference range for the right auricular parameters was put forward. The right auricular parameters had a good correlation with the right atrium volume, aortic diameter, the body weight, height, and body surface area but a bad correlation with the vertebral body height. Significantly (P < 0.05) greater values were found in the normal angle and distance in subjects below than over 40 years of age. No other significant (P > 0.05) difference existed in the other right auricular parameters. CONCLUSION: Quantitative measurements of the right auricle can help us get a good understanding of the right auricular morphology and its relationship with surrounding structures and are helpful for cardiac interventions of electrophysiology and radiofrequency ablation.


Assuntos
Apêndice Atrial/anatomia & histologia , Adulto , Idoso , Apêndice Atrial/diagnóstico por imagem , Angiografia por Tomografia Computadorizada/métodos , Angiografia Coronária/métodos , Feminino , Humanos , Processamento de Imagem Assistida por Computador , Masculino , Pessoa de Meia-Idade , Tomografia Computadorizada Multidetectores/métodos , Estudos Retrospectivos , Fatores Sexuais
17.
Surg Radiol Anat ; 39(6): 657-662, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-27864594

RESUMO

PURPOSE: To investigate the shape of right auricule on 256-slice computed tomography (CT). MATERIALS AND METHODS: Five hundred people (250 men, age range 16-84 years) who had cardiac multidetector CT angiography were recruited in this study. All patients had normal sinus rhythm with normal blood pressure (<140/90 mmHg for systolic/diastolic pressure). The morphology of the right auricule was studied and compared after reconstruction of the raw images. RESULTS: All patients successfully had cardiac CT angiography (100%), and the right auricule morphology was divided into five types and nine subtypes, including Type I of triangular shape (Ia and Ib), Type II of M shape (IIa and IIb), Type III of L shape (IIIa and IIIb), Type IV of reverse L shape (IVa and IVb), and Type V of balanced shape. The most common type of right auricule is Type IV (28.4%) followed by Type II (24.0%), whereas the least common is Type V (11.0%). Type Ia was present significantly (P < 0.0001) more frequently in females than in males, whereas Type IIa significantly (P = 0.042) more frequently in males than females. No other significant (P > 0.05) sex difference existed in the constitution ratio of the types. The normal angle was greater in Type Ib than in Ia. The greater the normal angle in Type I, the greater the deviation of the right auricule tip towards the left. CONCLUSION: A good understanding of the right auricule anatomical morphology can better guide atrial pacing, radiofrequency ablation and other surgical procedures while preventing possible intra-procedural complications.


Assuntos
Átrios do Coração/diagnóstico por imagem , Tomografia Computadorizada Multidetectores/métodos , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Angiografia por Tomografia Computadorizada , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Interpretação de Imagem Radiográfica Assistida por Computador , Estudos Retrospectivos
18.
J Magn Reson Imaging ; 44(5): 1143-1150, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27015960

RESUMO

PURPOSE: To quantitatively investigate left ventricular volume and function in middle-aged healthy subjects. MATERIALS AND METHODS: Ninety healthy volunteers underwent cardiac 3 Tesla MRI. The left ventricular end-diastolic volume (EDV) and end-systolic volume (ESV), stroke volume (SV), ejection fraction (EF), cardiac output (CO), myocardial mass (MM), and their normalized indices (EDVI, ESVI, SVI, CI, and MI, respectively) after corrected with the body surface area (BSA) were analyzed and compared at different ages. RESULTS: All subjects had successfully completed the 3-Tesla cardiac MR. Females had significantly smaller EDV (110.5 ± 9.2 versus 125.7 ± 8.3 mL), ESV (36.1 ± 3.5 versus 41.5 ± 3.8 mL), SV (74.3 ± 6.3 versus 84.2 ± 6.7 mL), CO (5.4 ± 0.8 versus 5.8 ± 0.9 l/min) and MM (73.0 ± 10.5 versus 94.8 ± 10.6 g) than males (P < 0.05). The EF had no significant (P = 0.47) difference between genders (67.3 ± 1.7 percent in females versus 66.9 ± 2.4 percent in males). After normalization with BSA, no significant (P > 0.05) difference was detected between the genders in EDVI (71.2 ± 4.3 versus 71.1 ± 4.2 mL/m2 , P = 0.882), ESVI (23.3 ± 1.9 versus 23.5 ± 1.9 mL/m2 , P = 0.733) and SVI (47.9 ± 2.9 versus 47.7 ± 3.7 mL/m2 , P = 0.698) except for CI and MI. Females had significantly (P < 0.05) greater CI (3.5 ± 0.4 versus 3.3 ± 0.4) but smaller MI (46.9 ± 5.3 versus 53.6 ± 7.6) than males. EDV, EDVI, ESV, ESVI, SV, and SVI significantly (P < 0.05) decreased with age increase. BSA was positively correlated with EDV, ESV, SV, MM, and CO. No significance (P > 0.05) was detected in other parameters. CONCLUSION: The left ventricular volume and function differs in women compared with men in the middle-aged population, and these parameters have a tendency of decrease with ageing. J. Magn. Reson. Imaging 2016;44:1143-1150.


Assuntos
Envelhecimento/fisiologia , Ventrículos do Coração/diagnóstico por imagem , Imageamento por Ressonância Magnética/métodos , Volume Sistólico/fisiologia , Função Ventricular Esquerda/fisiologia , Adulto , Distribuição por Idade , Idoso , Envelhecimento/patologia , China/epidemiologia , Feminino , Ventrículos do Coração/anatomia & histologia , Humanos , Imageamento por Ressonância Magnética/estatística & dados numéricos , Masculino , Pessoa de Meia-Idade , Valores de Referência , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Distribuição por Sexo
19.
Int J Syst Evol Microbiol ; 66(3): 1358-1363, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26755354

RESUMO

A novel strain of actinobacteria, designated strain NEAU-ZJC8T, was isolated from a saline-alkaline soil collected from Heilongjiang Province, north-east China and characterized using a polyphasic approach. Strain NEAU-ZJC8T exhibited morphological, cultural and chemotaxonomic features consistent with its classification as representing a member of the genus Streptomyces. Growth occurred at 16-35 °C, pH 5.0-11.0 and in the presence of 0-11 % (w/v) NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid and glycine. Whole-cell hydrolysates mainly contained glucose, galactose and ribose. Predominant menaquinones were MK-9(H6), MK-9(H4) and MK-9(H8). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified phospholipids. The major cellular fatty acids (>10 %) were iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and C16 : 0. The G+C content of the DNA was 72.7 mol%. A phylogenetic tree based on 16S rRNA sequences showed that strain NEAU-ZJC8T formed a distinct clade within the genus Streptomyces and was closely related to Streptomyces haliclonae DSM 41970T (98.56 % similarity) and Streptomyces marinus NBRC 105047T (97.96 % similarity). A combination of DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-ZJC8T could be distinguished from its closest phylogenetic relatives. Therefore, strain NEAU-ZJC8T represents a novel species of the genus Streptomyces, for which the name Streptomyces daqingensis sp. nov. is proposed. The type strain is NEAU-ZJC8T ( = CGMCC 4.7178T = JCM 30057T).

20.
Antonie Van Leeuwenhoek ; 109(3): 439-48, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26767659

RESUMO

Three novel actinobacteria, designated strains NEAU-FSHN1(T), NEAU-hd-3(T) and NEAU-Y6(T), were isolated from a stream base, soil adjacent to the stream and a root of Corydalis yanhusuo L, respectively, collected from Wuchang, Heilongjiang Province, China. A polyphasic study was carried out to establish the taxonomic positions of these strains. The three strains were observed to form scant aerial hyphae that differentiated into spherical spore vesicles. The phylogenetic analysis based on the 16S rRNA gene sequences of strains NEAU-FHSN1(T), NEAU-hd-3(T) and NEAU-Y6(T) showed that the three novel isolates exhibit 99.2 % (NEAU-FHSN1(T)/NEAU-hd-3(T)), 99.2 % (NEAU-FHSN1(T)/NEAU-Y6(T)) and 99.7 % (NEAU-hd-3(T)/NEAU-Y6(T)) 16S rRNA gene sequence similarities with each other and that they are closely related to strains Streptosporangium shengliense NEAU-GH7(T) (sequence similarities 98.72, 98.85, 98.99 %), Streptosporangium roseum DSM 43021(T) (98.65, 98.51, 98.58 %) and Streptosporangium album DSM 43023(T) (98.41, 98.96, 98.89 %). However, the DNA-DNA hybridization values between strains NEAU-FSHN1(T), NEAU-hd-3(T) and NEAU-Y6(T) were 61.2 % (NEAU-FSHN1(T)/NEAU-hd-3(T)), 63.5 % (NEAU-FHSN1(T)/NEAU-Y6(T)) and 65.8 % (NEAU-hd-3(T)/NEAU-Y6(T)), and the values between the three strains and their close phylogenetic relatives were also below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA-DNA hybridization results, the three strains can be distinguished from each other and their close phylogenetic relatives. Thus, strains NEAU-FHSN1(T), NEAU-hd-3(T) and NEAU-Y6(T) are concluded to represent three novel species of the genus Streptosporangium, for which the names Streptosporangium lutulentum sp. nov., Streptosporangium fenghuangense sp. nov. and Streptosporangium corydalis sp. nov. are proposed. The type strains are NEAU-FHSN1(T) (=CGMCC 4.7141(T) = DSM 46740(T)), NEAU-Y6(T) (=CGMCC 4.7150(T) = DSM 46722(T)) and NEAU-hd3(T) (CGMCC 4.7212(T) = JCM 30058(T)), respectively.


Assuntos
Actinobacteria/classificação , Meio Ambiente , Microbiologia Ambiental , Actinobacteria/genética , Actinobacteria/isolamento & purificação , Actinobacteria/ultraestrutura , Técnicas de Tipagem Bacteriana , Composição de Bases , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
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