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de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. CELL GENOMICS 2024; 4:100527. [PMID: 38537634 PMCID: PMC11019364 DOI: 10.1016/j.xgen.2024.100527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 02/29/2024] [Indexed: 04/09/2024]
Abstract
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Affiliation(s)
- Tristan V de Jong
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Chris Benner
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - William Chow
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Wendy M Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Peter A Doris
- The Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hakan M Gunturkun
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Guryev
- Genome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Jun Huang
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA
| | - Panjun Kim
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ling Li
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Pejman Mohammadi
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jennifer R Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hongyang Wang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Burt M Sharp
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Francesca Telese
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
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Uchida A, Kidokoro K, Sogawa Y, Itano S, Nagasu H, Satoh M, Sasaki T, Kashihara N. 5-Aminolevulinic acid exerts renoprotective effect via Nrf2 activation in murine rhabdomyolysis-induced acute kidney injury. Nephrology (Carlton) 2019; 24:28-38. [PMID: 29068550 DOI: 10.1111/nep.13189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2017] [Indexed: 01/04/2023]
Abstract
AIM Acute kidney injury (AKI) is associated with chronic kidney disease, as well as high mortality, but effective treatments for AKI are still lacking. A recent study reported the prevention of renal injury, such as ischemia-reperfusion injury, by 5-aminolevulinic acid (ALA), which induces an antioxidant effect. The current study aimed to investigate the effect of ALA in a rhabdomyolysis-induced mouse model of AKI created by intramuscular injection of 50% glycerol. METHODS Rhabdomyolysis-induced AKI was induced by an intramuscular injection of glycerol (5 mL/kg body weight) into mice. Administration of ALA (30 mg/kg, by gavage) was started from 48 h before or 24 h after glycerol injection. The mice were sacrificed at 72 h after glycerol injection. The roles of nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1), which is one of the Nrf2-related antioxidants, were further investigated through in vivo and in vitro methods. RESULTS 5-aminolevulinic acid markedly reduced renal dysfunction and tubular damage in mice with rhabdomyolysis-induced AKI. ALA administration decreased oxidative stress, macrophage infiltration, and inflammatory cytokines and apoptosis. The expression of Nrf2 was upregulated by ALA administration. However, administration of Zinc protoporphyrin-9 (ZnPPIX) to inhibit HO-1 activity did not abolish these improvements by ALA. The expression of Nrf2-associated antioxidant factors other than HO-1 was also increased. CONCLUSION These findings indicate that ALA exerts its antioxidant activity via Nrf2-associated antioxidant factors to provide a renoprotective effect against rhabdomyolysis-induced AKI.
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Affiliation(s)
- Atsushi Uchida
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Japan
| | - Kengo Kidokoro
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Japan
| | - Yuji Sogawa
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Japan
| | - Seiji Itano
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Japan
| | - Hajime Nagasu
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Japan
| | - Minoru Satoh
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Japan
| | - Tamaki Sasaki
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Japan
| | - Naoki Kashihara
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Japan
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Yuluğ E, Türedi S, Yıldırım Ö, Yenilmez E, Aliyazıcıoğlu Y, Demir S, Özer-Yaman S, Menteşe A. Biochemical and morphological evaluation of the effects of propolis on cisplatin induced kidney damage in rats. Biotech Histochem 2018; 94:204-213. [PMID: 30512970 DOI: 10.1080/10520295.2018.1543895] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cisplatin (CP) is a chemotherapeutic agent used to treat various types of cancer; nephrotoxicity is the most common adverse effect of the drug. We investigated the protective effects of propolis against CP induced kidney injury. Thirty-six male rats were divided into six equal groups: untreated control group, 50 mg/kg/day propolis group, 100 mg/kg/day propolis group, single-dose 7 mg/kg CP group, 7 mg/kg CP + 50 mg/kg/day propolis and 7 mg/kg CP + 100 mg/kg propolis. Rats were sacrificed after 14 days and kidneys were removed for histopathological and biochemical analyses. We used hematoxylin & eosin and periodic acid-Schiff staining to evaluate kidney histopathology and we used the TUNEL technique to assess apoptosis. We also measured total oxidant status (TOS), total antioxidant status (TAS), oxidative stress index (OSI), ischemia-modified albumin (IMA) and malondialdehyde (MDA) levels in tissue and blood specimens. Normal morphology was observed in the control, 50 mg/kg/day propolis and 100 mg/kg/day propolis groups by light microscopy. Degeneration of tubule cells, edema and tubule dilation were increased in the CP group compared to the control group. Degeneration of tubule cells and dilation of Bowman's spaces were decreased in the CP + 50 mg/kg/day propolis and CP + 100 mg/kg/day propolis groups compared to the CP group. Tubule dilation decreased significantly in the CP + 100 mg/kg propolis group compared to the CP group. Also, the 7 mg/kg CP group exhibited altered proximal tubule epithelial cells, loss of brush border and thickening of the parietal layer of Bowman's capsule in glomeruli and basal laminae of tubules. A normal brush border was observed in the CP + 50 mg/kg/day propolis and CP + 100 mg/kg/day groups. Serum OSI and MDA levels were increased in the CP group compared to the control group. Serum MDA levels decreased significantly in the CP + 50 mg/kg/day propolis and 100 mg/kg CP + propolis groups compared to the CP group. CP caused significant damage to kidney tissue; propolis exhibited dose-dependent prevention of tissue damage.
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Affiliation(s)
- E Yuluğ
- a Department of Histology and Embryology, Faculty of Medicine , Karadeniz Technical University , Trabzon , Turkey
| | - S Türedi
- b Department of Histology and Embryology, Faculty of Medicine , Harran University , Şanlıurfa , Turkey
| | - Ö Yıldırım
- a Department of Histology and Embryology, Faculty of Medicine , Karadeniz Technical University , Trabzon , Turkey
| | - E Yenilmez
- a Department of Histology and Embryology, Faculty of Medicine , Karadeniz Technical University , Trabzon , Turkey
| | - Y Aliyazıcıoğlu
- c Department of Medical Biochemistry, Faculty of Medicine , Karadeniz Technical University , Trabzon , Turkey
| | - S Demir
- d Department of Nutrition and Dietetics, Faculty of Health Sciences , Karadeniz Technical University , Trabzon , Turkey
| | - S Özer-Yaman
- c Department of Medical Biochemistry, Faculty of Medicine , Karadeniz Technical University , Trabzon , Turkey
| | - A Menteşe
- e Program of Medical Laboratory Techniques, Vocational School of Health Sciences , Karadeniz Technical University , Trabzon , Turkey
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Chen S, Zhu Y, Liu Z, Gao Z, Li B, Zhang D, Zhang Z, Jiang X, Liu Z, Meng L, Yang Y, Shi B. Grape Seed Proanthocyanidin Extract Ameliorates Diabetic Bladder Dysfunction via the Activation of the Nrf2 Pathway. PLoS One 2015; 10:e0126457. [PMID: 25974036 PMCID: PMC4431834 DOI: 10.1371/journal.pone.0126457] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/03/2015] [Indexed: 01/11/2023] Open
Abstract
Diabetes Mellitus (DM)-induced bladder dysfunction is predominantly due to the long-term oxidative stress caused by hyperglycemia. Grape seed proanthocyanidin extract (GSPE) has been reported to possess a broad spectrum of pharmacological and therapeutic properties against oxidative stress. However, its protective effects against diabetic bladder dysfunction have not been clarified. This study focuses on the effects of GSPE on bladder dysfunction in diabetic rats induced by streptozotocin. After 8 weeks of GSPE administration, the bladder function of the diabetic rats was improved significantly, as indicated by both urodynamics analysis and histopathological manifestation. Moreover, the disordered activities of antioxidant enzymes (SOD and GSH-Px) and abnormal oxidative stress levels were partly reversed by treatment with GSPE. Furthermore, the level of apoptosis in the bladder caused by DM was decreased following the administration of GSPE according to the Terminal Deoxynucleotidyl Transferase (TdT)-mediated dUTP Nick-End Labeling (TUNEL) assay. Additionally, GSPE affected the expression of apoptosis-related proteins such as Bax, Bcl-2 and cleaved caspase-3. Furthermore, GSPE showed neuroprotective effects on the bladder of diabetic rats, as shown by the increased expression of nerve growth factor (NGF) and decreased expression of the precursor of nerve growth factor (proNGF). GSPE also activated nuclear erythroid2-related factor2 (Nrf2), which is a key antioxidative transcription factor, with the concomitant elevation of downstream hemeoxygenase-1 (HO-1). These findings suggested that GSPE could ameliorate diabetic bladder dysfunction and decrease the apoptosis of the bladder in diabetic rats, a finding that may be associated with its antioxidant activity and ability to activate the Nrf2 defense pathway.
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Affiliation(s)
- Shouzhen Chen
- Department of Urology, Qilu Hospital of Shandong University, Wenhua Xi Road, Jinan, Shandong Province, People’s Republic of China
| | - Yaofeng Zhu
- Department of Urology, Qilu Hospital of Shandong University, Wenhua Xi Road, Jinan, Shandong Province, People’s Republic of China
| | - Zhifeng Liu
- Department of Urology, Qilu Hospital of Shandong University, Wenhua Xi Road, Jinan, Shandong Province, People’s Republic of China
- Department of Urology, The Central Hospital of Tai’ an, Longtan Road, Tai’ an, Shandong Province, People’s Republic of China
| | - Zhaoyun Gao
- Department of Urology, People’s Hospital of Yinan County, Lishan Road, Yinan, Shandong Province, People’s Republic of China
| | - Baoying Li
- Department of Geriatrics, Qilu Hospital of Shandong University, Wenhua Xi Road, Jinan, Shandong Province, People’s Republic of China
| | - Dongqing Zhang
- Department of Urology, Qilu Hospital of Shandong University, Wenhua Xi Road, Jinan, Shandong Province, People’s Republic of China
| | - Zhaocun Zhang
- Department of Urology, Qilu Hospital of Shandong University, Wenhua Xi Road, Jinan, Shandong Province, People’s Republic of China
| | - Xuewen Jiang
- Department of Urology, Qilu Hospital of Shandong University, Wenhua Xi Road, Jinan, Shandong Province, People’s Republic of China
| | - Zhengfang Liu
- Department of Urology, Qilu Hospital of Shandong University, Wenhua Xi Road, Jinan, Shandong Province, People’s Republic of China
| | - Lingquan Meng
- Department of Urology, Qilu Hospital of Shandong University, Wenhua Xi Road, Jinan, Shandong Province, People’s Republic of China
| | - Yue Yang
- Department of Urology, Qilu Hospital of Shandong University, Wenhua Xi Road, Jinan, Shandong Province, People’s Republic of China
| | - Benkang Shi
- Department of Urology, Qilu Hospital of Shandong University, Wenhua Xi Road, Jinan, Shandong Province, People’s Republic of China
- * E-mail:
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