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1.
Mol Biol Evol ; 39(12)2022 12 05.
Artigo em Inglês | MEDLINE | ID: mdl-36458838

RESUMO

The Angiosperms353 gene set (AGS) consists of a set of 353 universal low-copy nuclear genes that were selected by examining more than 600 angiosperm species. These genes can be used for phylogenetic studies and population genetics at multiple taxonomic scales. However, current pipelines are not able to recover Angiosperms353 genes efficiently and accurately from high-throughput sequences. Here, we developed Easy353, a reference-guided assembly tool to recover the AGS from high-throughput sequencing (HTS) data (including genome skimming, RNA-seq, and target enrichment). Easy353 is an open-source user-friendly assembler for diverse types of high-throughput data. It has a graphical user interface and a command-line interface that is compatible with all widely-used computer systems. Evaluations, based on both simulated and empirical data, suggest that Easy353 yields low rates of assembly errors.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Software , Filogenia , Genoma
2.
Mol Nutr Food Res ; 66(23): e2200447, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36214059

RESUMO

SCOPE: Non-alcoholic fatty liver disease (NAFLD) is a type of metabolic syndrome characterized of abnormal lipid deposition in the liver. Adlay polyphenol (AP), an effective component extracted from Coix lacryma-jobi L., has been reported that it can be used as a dietary supplement to prevent NAFLD. In this study, the mechanism and action of AP on lipid metabolism and regulation of intestinal flora are investigated. METHODS AND RESULTS: AP significantly decreases the lipid accumulation in free fatty acid-treated HepG2 cells. Western blot results indicate that AP improves lipid metabolism via activating the p-AMPK/p-ACC pathway. In vivo experiments show AP treatment significantly decreases the body weight, liver weight, hepatic triglyceride, and total cholesterol contents, as well as the serum glucose levels in high fat diet-fed mice, which may affect lipid accumulation by activating AMPK pathway and changing intestinal bacterial communities and intestinal microbiome metabolism. CONCLUSION: AP can be used as a food supplement for improving lipid metabolic dysfunction and reducing the incidence of metabolic diseases.


Assuntos
Coix , Microbioma Gastrointestinal , Hipercolesterolemia , Hepatopatia Gordurosa não Alcoólica , Camundongos , Animais , Coix/metabolismo , Polifenóis/farmacologia , Polifenóis/metabolismo , Hepatopatia Gordurosa não Alcoólica/etiologia , Proteínas Quinases Ativadas por AMP/metabolismo , Glucose/metabolismo , Fígado/metabolismo , Metabolismo dos Lipídeos , Triglicerídeos/metabolismo , Hipercolesterolemia/metabolismo , Homeostase
3.
Int J Biol Macromol ; 188: 180-196, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34339782

RESUMO

Gingival crevicular fluid (GCF) is a physiological fluid and an inflammatory serum exudate derived from the gingival plexus of blood vessels and mixed with host tissues and subgingival plaque flows. In addition to proteins, GCF contains a diverse population of cells, including desquamated epithelial cells, cytokines, electrolytes, and bacteria from adjacent plaques. Recently, matrix metalloproteinases(MMPs), which are endopeptidases that are active against extracellular macromolecules, in GCF have been revealed as potential utility biomarkers for the diagnosis and follow-up of oral and systemic diseases, thereby facilitating the early evaluation of malignancy risk and the monitoring of disease progression and treatment response. Tissue inhibitors of metalloproteinases (TIMPs) are specific inhibitors of matrixins that participate in the regulation of local activities of MMPs in tissues. This review provides an overview of the latest findings on the diagnostic and prognostic values of MMPs and TIMPs in GCF of oral and systemic diseases, including periodontal disease, pulpitis, peri-implantitis and cardiovascular disease as well as the extraction, detection and analytical methods for GCF.


Assuntos
Biomarcadores/metabolismo , Gengiva/metabolismo , Líquido do Sulco Gengival/metabolismo , Inibidores Teciduais de Metaloproteinases/isolamento & purificação , Doenças Cardiovasculares/diagnóstico , Células Epiteliais/metabolismo , Humanos , Peri-Implantite/diagnóstico , Doenças Periodontais/diagnóstico , Periodontite/diagnóstico , Pulpite/diagnóstico , Inibidores Teciduais de Metaloproteinases/genética
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