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      Dieting alleviates hyperuricemia and organ injuries in uricase-deficient rats via down-regulating cell cycle pathway

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          Abstract

          Dieting is a basic treatment for lowering hyperuricemia. Here, we aimed to determine the optimal amount of dietary food that lowers serum uric acid (SUA) without modifying the dietary ingredients in rats. Increased SUA was found in food-deprived 45-day-old uricase-deficient rats (Kunming-DY rats), and the optimal amount of dietary food (75% dietary intake) to lower SUA was established by controlling the amount of food given daily from 25% to 100% for 2 weeks. In addition to lowering SUA by approximately 22.5 ± 20.5%, the optimal amount of dietary food given for 2 weeks inhibited urine uric acid excretion, lowered the uric acid content in multiple organs, improved renal function, lowered serum triglyceride, alleviated organ injuries ( e.g., liver, kidney and intestinal tract) at the histological level, and down-regulated the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway of the cell cycle (ko04110). Taken together, these results demonstrate that 75% dietary food effectively lowers the SUA level without modifying dietary ingredients and alleviates the injuries resulting from uricase deficiency or hyperuricemia, the mechanism of which is associated with the down-regulation of the cell cycle pathway.

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          clusterProfiler: an R package for comparing biological themes among gene clusters.

          Guangchuang Yu, Li-Gen Wang, Yanyan Han … (2012)
          Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.
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            KEGG: kyoto encyclopedia of genes and genomes.

            M Kanehisa (2000)
            KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).
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              Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms

              Cole Trapnell, Brian A Williams, Geo M Pertea … (2013)
              High-throughput mRNA sequencing (RNA-Seq) holds the promise of simultaneous transcript discovery and abundance estimation 1-3 . We introduce an algorithm for transcript assembly coupled with a statistical model for RNA-Seq experiments that produces estimates of abundances. Our algorithms are implemented in an open source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed more than 430 million paired 75bp RNA-Seq reads from a mouse myoblast cell line representing a differentiation time series. We detected 13,692 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Analysis of transcript expression over the time series revealed complete switches in the dominant transcription start site (TSS) or splice-isoform in 330 genes, along with more subtle shifts in a further 1,304 genes. These dynamics suggest substantial regulatory flexibility and complexity in this well-studied model of muscle development.
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                Author and article information

                Contributors
                Weigang Duan
                Journal
                Journal ID (nlm-ta): PeerJ
                Journal ID (iso-abbrev): PeerJ
                Journal ID (publisher-id): peerj
                Title: PeerJ
                Publisher: PeerJ Inc. (San Diego, USA )
                ISSN (Electronic): 2167-8359
                Publication date (Electronic): 8 September 2023
                Publication date Collection: 2023
                Volume: 11
                Electronic Location Identifier: e15999
                Affiliations
                [1 ]School of Basic Medicine, Kunming Medical University , Kunming, Yunnan, China
                [2 ]School of Chinese Medicine, Yunnan University of Traditional Chinese Medicne , Kunming, Yunnan, China
                [3 ]School of Basic Medicine, Yunnan University of Traditional Chinese Medicine , Kunming, Yunnan, China
                [4 ]The Third Affiliated Hospital, Yunnan University of Traditional Chinese Medicine , Kunming, Yunnan, China
                Article
                Publisher ID: 15999
                DOI: 10.7717/peerj.15999
                PMC ID: 10494837
                PubMed ID: 37701826
                SO-VID: 47d0f08e-7622-450d-bd4d-2f04ab49b07b
                Copyright © ©2023 Yu et al.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                Date received : 19 April 2023
                Date accepted : 9 August 2023
                Funding
                Funded by: National Natural Science Foundation of China
                Award ID: 82260886
                Funded by: Yunnan Provincial Science and Technology Department–Applied Basic Research Joint Special Funds of Kunming Medical University
                Award ID: 202101AY070001-007
                Funded by: Yunnan Provincial Science and Technology Department–Applied Basic Research Joint Special Funds of Yunnan University of Traditional Chinese Medicine
                Award ID: 202101AZ070001-010
                Award ID: 202101AZ070001-093
                Award ID: 202101AZ070001-242
                The work was financially supported by the National Natural Science Foundation of China (No. 82260886), the Yunnan Provincial Science and Technology Department–Applied Basic Research Joint Special Funds of Kunming Medical University (202101AY070001-007), and the Yunnan Provincial Science and Technology Department–Applied Basic Research Joint Special Funds of Yunnan University of Traditional Chinese Medicine (202101AZ070001-010, 202101AZ070001-093, 202101AZ070001-242). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Food Science and Technology
                Subject: Urology
                Subject: Metabolic Sciences

                Keywords: uricase-deficient rats,hyperuricemia,serum uric acid,dieting,fasting,renal injury,cell cycle pathway
                Data availability:
                Keywords: uricase-deficient rats, hyperuricemia, serum uric acid, dieting, fasting, renal injury, cell cycle pathway

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