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Vedi M, Smith JR, Thomas Hayman G, Tutaj M, Brodie KC, De Pons JL, Demos WM, Gibson AC, Kaldunski ML, Lamers L, Laulederkind SJF, Thota J, Thorat K, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. 2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource. Genetics 2023; 224:iyad042. [PMID: 36930729 PMCID: PMC10474928 DOI: 10.1093/genetics/iyad042] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
The Rat Genome Database (RGD, https://rgd.mcw.edu) has evolved from simply a resource for rat genetic markers, maps, and genes, by adding multiple genomic data types and extensive disease and phenotype annotations and developing tools to effectively mine, analyze, and visualize the available data, to empower investigators in their hypothesis-driven research. Leveraging its robust and flexible infrastructure, RGD has added data for human and eight other model organisms (mouse, 13-lined ground squirrel, chinchilla, naked mole-rat, dog, pig, African green monkey/vervet, and bonobo) besides rat to enhance its translational aspect. This article presents an overview of the database with the most recent additions to RGD's genome, variant, and quantitative phenotype data. We also briefly introduce Virtual Comparative Map (VCMap), an updated tool that explores synteny between species as an improvement to RGD's suite of tools, followed by a discussion regarding the refinements to the existing PhenoMiner tool that assists researchers in finding and comparing quantitative data across rat strains. Collectively, RGD focuses on providing a continuously improving, consistent, and high-quality data resource for researchers while advancing data reproducibility and fulfilling Findable, Accessible, Interoperable, and Reusable (FAIR) data principles.
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Affiliation(s)
- Mahima Vedi
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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2
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A modified heterotopic heart transplantation in the rat - as an important model in experimental regeneration and replacement of the failing organ. POLISH JOURNAL OF THORACIC AND CARDIOVASCULAR SURGERY 2020; 17:149-154. [PMID: 33014091 PMCID: PMC7526486 DOI: 10.5114/kitp.2020.99079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/15/2020] [Indexed: 11/17/2022]
Abstract
The qualification of new knowledge is one of the oldest problems in experimental medicine that provides a link between fundamental discovery, hypothesis, ‘proof of concept’ preclinical studies and development of clinical trials. The biggest challenge in animal models is the proper evaluation of all the aspects that are crucial in specific studied pathologies as well as the prediction of their progression. The aim of this review was to describe and discuss the rat animal model of heart transplant. The rat model of heart transplantation is an excellent yet underestimated method of research of prevention, monitoring and treatment of acute and chronic, immune and nonimmune response to organ transplantation. Despite being a technically and logistically demanding model, it provides a tool for reproducible experiments with longterm animal survival and excellent graft survival.
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Zhao Y, Smith JR, Wang SJ, Dwinell MR, Shimoyama M. Quantitative phenotype analysis to identify, validate and compare rat disease models. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5424140. [PMID: 30938777 PMCID: PMC6444380 DOI: 10.1093/database/baz037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/08/2019] [Accepted: 02/27/2019] [Indexed: 12/18/2022]
Abstract
The laboratory rat has been widely used as an animal model in biomedical research. There are many strains exhibiting a wide variety of phenotypes. Capturing these phenotypes in a centralized database provides researchers with an easy method for choosing the appropriate strains for their studies. Existing resources have provided some preliminary work in rat phenotype databases. However, existing resources suffer from problems such as small number of animals, lack of updating, web interface queries limitations and lack of standardized metadata. The Rat Genome Database (RGD) PhenoMiner tool has provided the first step in this effort by standardizing and integrating data from individual studies. Our work, mainly utilizing data curated in RGD, involves the following key steps: (i) we developed a meta-analysis pipeline to automatically integrate data from heterogeneous sources and to produce expected ranges (standardized phenotype ranges) for different strains and phenotypes under different experimental conditions; (ii) we created tools to visualize expected ranges for individual strains and strain groups. We developed a meta-analysis pipeline and an interactive web interface that summarizes and visualizes expected ranges produced from the meta-analysis pipeline. Automation of the pipeline allows for updates as additional data becomes available. The interactive web interface provides curators and researchers with a platform for identifying and validating expected ranges for a variety of quantitative phenotypes. The data analysis result and visualization tools will promote an understanding of rat disease models, guide researchers to choose optimal strains for their research needs and encourage data sharing from different research hubs. Such resources also help to promote research reproducibility. The interactive platforms created in this project will continue to provide a valuable resource for translational research efforts.
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Affiliation(s)
- Yiqing Zhao
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Jennifer R Smith
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Shur-Jen Wang
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Mary Shimoyama
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
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4
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Wang D, Wang Y, Liu H, Tong C, Ying Q, Sachinidis A, Li L, Peng L. Laminin promotes differentiation of rat embryonic stem cells into cardiomyocytes by activating the integrin/FAK/PI3K p85 pathway. J Cell Mol Med 2019; 23:3629-3640. [PMID: 30907509 PMCID: PMC6484303 DOI: 10.1111/jcmm.14264] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 12/27/2022] Open
Abstract
The generation of germline competent rat embryonic stem cells (rESCs) allows the study of their lineage commitment. Here, we developed a highly efficient system for rESC-derived cardiomyocytes, and even the formation of three-dimensional (3D)-like cell clusters with cTNT and α-Actinin. We have validated that laminin can interact with membrane integrin to promote the phosphorylation of both phosphatidylinositol 3-kinase (PI3K) p85 and the focal adhesion kinase (FAK). In parallel, GATA4 was up-regulated. Upon inhibiting the integrin, laminin loses the effect on cardiomyocyte differentiation, accompanied with a down-regulation of phosphorylation level of PI3K p85 and FAK. Meanwhile, the expression of Gata4 was inhibited as well. Taken together, laminin is a crucial component in the differentiation of rESCs into cardiomyocytes through increasing their proliferation via interacting with integrin pathway. These results provide new insights into the pathways mediated by extracellular laminin involved in the fate of rESC-derived cardiomyocytes.
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Affiliation(s)
- Duo Wang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Yumei Wang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Huan Liu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Chang Tong
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qilong Ying
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Agapios Sachinidis
- Institute of Neurophysiology and Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Li Li
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Luying Peng
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
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Abstract
Resources for rat researchers are extensive, including strain repositories and databases all around the world. The Rat Genome Database (RGD) serves as the primary rat data repository, providing both manual and computationally collected data from other databases.
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Species generalization and differences in Hedgehog pathway regulation of fungiform and circumvallate papilla taste function and somatosensation demonstrated with sonidegib. Sci Rep 2018; 8:16150. [PMID: 30385780 PMCID: PMC6212413 DOI: 10.1038/s41598-018-34399-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/09/2018] [Indexed: 01/20/2023] Open
Abstract
Species generalization in the profound, modality-specific effects of Hedgehog pathway inhibition (HPI) in taste organ homeostasis and sensation is shown. With the HPI, cancer drug sonidegib, we demonstrate that the rat taste system, in addition to mouse, is regulated by Hedgehog signaling. After sonidegib treatment for 16–36 days in rat, there is loss of taste buds (TB) in soft palate, in fungiform (FP) and circumvallate papillae (CV), and elimination of taste responses from chorda tympani and glossopharyngeal nerves. The retained innervation in FP and CV during HPI cannot sustain TB. Responses to tactile stimuli are not altered, and temperature responses are reduced only after 28 days treatment, demonstrating modality-specific effects. Rat FP and neural effects are similar to those in mouse whereas TB and neural response effects from the rat CV are much more severe. When recovery is introduced in mouse after prolonged, 48 days HPI, the TB in CV are restored whereas those in FP are not. Overall, Hedgehog signaling regulation is shown to generalize to the rat taste system, and the modality-specific controls in taste organ sensation are affirmed. The reported, debilitating taste disturbances in patients who use HPI drugs can be better understood based on these data.
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7
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Wróbel PM, Bała S, Czyzycki M, Golasik M, Librowski T, Ostachowicz B, Piekoszewski W, Surówka A, Lankosz M. Combined micro-XRF and TXRF methodology for quantitative elemental imaging of tissue samples. Talanta 2016; 162:654-659. [PMID: 27837886 DOI: 10.1016/j.talanta.2016.10.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/07/2016] [Accepted: 10/08/2016] [Indexed: 01/17/2023]
Abstract
Local differences in structural properties of biological specimens pose a major limitation to quantitative X-ray fluorescence imaging. This is because both the various tissue compartments of different density and variation in the sample thickness upon frequently used freeze-drying come up with the different values of the sample mass per unit area to be taken into account. Even though several solutions to tackle this problem based on the home-made standards for quantification in terms of thickness- and density-independent elemental mass fractions have been proposed, this issue is not addressed enough due to the samples' heterogeneity. In our recent study, we propose a calculation scheme based on combined external-standard micro X-ray fluorescence (micro-XRF) imaging and internal-standard total reflection X-ray fluorescence (TXRF) analysis to determine the corrected elemental mass fraction distributions in commonly analysed rat tissues: kidney, liver and spleen. The results of TXRF analysis of digested large tissue sections together with the mean values of elemental masses per unit area obtained with micro-XRF were employed to determine the average masses per unit area of the samples. The correction for variation of the tissue thickness and density was done through with the use of Compton intensities. Importantly, by its versatility, our novel approach can be used to produce elemental contrast in a variety of biological specimens where local variations in either the sample density or thickness are no longer the issue.
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Affiliation(s)
- Paweł M Wróbel
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Mickiewicza 30, 30-059 Krakow, Poland
| | - Sławomir Bała
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Mickiewicza 30, 30-059 Krakow, Poland
| | - Mateusz Czyzycki
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Mickiewicza 30, 30-059 Krakow, Poland; Physics Section, Nuclear Science and Instrumentation Laboratory (NSIL), IAEA Laboratories, A-2444 Seibersdorf, Austria
| | - Magdalena Golasik
- Faculty of Chemistry, Jagiellonian University in Krakow, Ingardena 3, 30-060 Krakow, Poland
| | - Tadeusz Librowski
- Faculty of Chemistry, Jagiellonian University in Krakow, Ingardena 3, 30-060 Krakow, Poland; Faculty of Pharmacy, Medical College, Jagiellonian University in Krakow, Medyczna 9, 30-688 Krakow, Poland
| | - Beata Ostachowicz
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Mickiewicza 30, 30-059 Krakow, Poland
| | - Wojciech Piekoszewski
- Faculty of Chemistry, Jagiellonian University in Krakow, Ingardena 3, 30-060 Krakow, Poland
| | - Artur Surówka
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Mickiewicza 30, 30-059 Krakow, Poland
| | - Marek Lankosz
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Mickiewicza 30, 30-059 Krakow, Poland
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8
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Wang SJ, Laulederkind SJF, Hayman GT, Petri V, Smith JR, Tutaj M, Nigam R, Dwinell MR, Shimoyama M. Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database. Physiol Genomics 2016; 48:589-600. [PMID: 27287925 DOI: 10.1152/physiolgenomics.00046.2016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/08/2016] [Indexed: 01/18/2023] Open
Abstract
Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality.
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Affiliation(s)
- Shur-Jen Wang
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and
| | | | - G Thomas Hayman
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and
| | - Victoria Petri
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and
| | - Jennifer R Smith
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and
| | - Marek Tutaj
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and
| | - Rajni Nigam
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mary Shimoyama
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin; and
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9
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Smith JR, Park CA, Nigam R, Laulederkind SJF, Hayman GT, Wang SJ, Lowry TF, Petri V, Pons JD, Tutaj M, Liu W, Worthey EA, Shimoyama M, Dwinell MR. The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications. J Biomed Semantics 2013; 4:26. [PMID: 24103152 PMCID: PMC3882879 DOI: 10.1186/2041-1480-4-26] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 10/01/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The Clinical Measurement Ontology (CMO), Measurement Method Ontology (MMO), and Experimental Condition Ontology (XCO) were originally developed at the Rat Genome Database (RGD) to standardize quantitative rat phenotype data in order to integrate results from multiple studies into the PhenoMiner database and data mining tool. These ontologies provide the framework for presenting what was measured, how it was measured, and under what conditions it was measured. RESULTS There has been a continuing expansion of subdomains in each ontology with a parallel 2-3 fold increase in the total number of terms, substantially increasing the size and improving the scope of the ontologies. The proportion of terms with textual definitions has increased from ~60% to over 80% with greater synchronization of format and content throughout the three ontologies. Representation of definition source Uniform Resource Identifiers (URI) has been standardized, including the removal of all non-URI characters, and systematic versioning of all ontology files has been implemented. The continued expansion and success of these ontologies has facilitated the integration of more than 60,000 records into the RGD PhenoMiner database. In addition, new applications of these ontologies, such as annotation of Quantitative Trait Loci (QTL), have been added at the sites actively using them, including RGD and the Animal QTL Database. CONCLUSIONS The improvements to these three ontologies have been substantial, and development is ongoing. New terms and expansions to the ontologies continue to be added as a result of active curation efforts at RGD and the Animal QTL database. Use of these vocabularies to standardize data representation for quantitative phenotypes and quantitative trait loci across databases for multiple species has demonstrated their utility for integrating diverse data types from multiple sources. These ontologies are freely available for download and use from the NCBO BioPortal website at http://bioportal.bioontology.org/ontologies/1583 (CMO), http://bioportal.bioontology.org/ontologies/1584 (MMO), and http://bioportal.bioontology.org/ontologies/1585 (XCO), or from the RGD ftp site at ftp://rgd.mcw.edu/pub/ontology/.
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Affiliation(s)
- Jennifer R Smith
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Carissa A Park
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Rajni Nigam
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - G Thomas Hayman
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Shur-Jen Wang
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Timothy F Lowry
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Victoria Petri
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jeff De Pons
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Marek Tutaj
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Weisong Liu
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Elizabeth A Worthey
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Mary Shimoyama
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
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10
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Scott BB, Brody CD, Tank DW. Cellular resolution functional imaging in behaving rats using voluntary head restraint. Neuron 2013; 80:371-84. [PMID: 24055015 DOI: 10.1016/j.neuron.2013.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
Abstract
High-throughput operant conditioning systems for rodents provide efficient training on sophisticated behavioral tasks. Combining these systems with technologies for cellular resolution functional imaging would provide a powerful approach to study neural dynamics during behavior. Here we describe an integrated two-photon microscope and behavioral apparatus that allows cellular resolution functional imaging of cortical regions during epochs of voluntary head restraint. Rats were trained to initiate periods of restraint up to 8 s in duration, which provided the mechanical stability necessary for in vivo imaging while allowing free movement between behavioral trials. A mechanical registration system repositioned the head to within a few microns, allowing the same neuronal populations to be imaged on each trial. In proof-of-principle experiments, calcium-dependent fluorescence transients were recorded from GCaMP-labeled cortical neurons. In contrast to previous methods for head restraint, this system can be incorporated into high-throughput operant conditioning systems.
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Affiliation(s)
- Benjamin B Scott
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Bezos Center for Neural Circuit Dynamics, Princeton University, Princeton, NJ 08544, USA
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11
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Laulederkind SJF, Liu W, Smith JR, Hayman GT, Wang SJ, Nigam R, Petri V, Lowry TF, de Pons J, Dwinell MR, Shimoyama M. PhenoMiner: quantitative phenotype curation at the rat genome database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat015. [PMID: 23603846 PMCID: PMC3630803 DOI: 10.1093/database/bat015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses >40 000 rat gene records as well as human and mouse orthologs, >2000 rat and 1900 human quantitative trait loci (QTLs) records and >2900 rat strain records. Biological information curated for these data objects includes disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components. Recently, a project was initiated at RGD to incorporate quantitative phenotype data for rat strains, in addition to the currently existing qualitative phenotype data for rat strains, QTLs and genes. A specialized curation tool was designed to generate manual annotations with up to six different ontologies/vocabularies used simultaneously to describe a single experimental value from the literature. Concurrently, three of those ontologies needed extensive addition of new terms to move the curation forward. The curation interface development, as well as ontology development, was an ongoing process during the early stages of the PhenoMiner curation project. Database URL:http://rgd.mcw.edu
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Affiliation(s)
- Stanley J F Laulederkind
- Human and Molecular Genetics Center, Medical College of Wisconsin, Human and Molecular Genetics Center, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA.
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12
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Ayabe H, Ikeda S, Maruyama S, Shioyama S, Kikuchi M, Kawaguchi A, Yamada T, Ikeda T. Development of an efficient genotyping method to detect obese mutation in the mouse leptin gene for use in SPF barrier facilities. J Vet Med Sci 2012; 75:633-8. [PMID: 23229540 DOI: 10.1292/jvms.12-0348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have developed a rapid and efficient genotyping method for detection of the mouse leptin obese mutation (Lep(ob)) using tetra-primer amplification refractory mutation system-polymerase chain reaction (tetra-primer ARMS-PCR). In this method, whole blood collected onto gamma-ray sterilized Flinders Technology Associates (FTA) filter paper is used as PCR template without a DNA purification step. Three genotypes (Lep(ob)/Lep(ob), Lep(ob)/+ and +/+) differentiated by single-tube PCR and electrophoresis were perfectly consistent with those determined by PCR-restriction fragment length polymorphism (PCR-RFLP). This method can save material costs and operation time, because it does not require restriction enzyme digestion and could be set up in most specific pathogen-free (SPF) barrier facilities.
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Affiliation(s)
- Hiroaki Ayabe
- Production Department, Plasma Team, Charles River Laboratories Japan, Inc., 795 Shimofurusawa, Atsugi-shi, Kanagawa 243-0214, Japan.
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13
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Blædel M, Raun K, Boonen HCM, Sheykhzade M, Sams A. Early onset inflammation in pre-insulin-resistant diet-induced obese rats does not affect the vasoreactivity of isolated small mesenteric arteries. Pharmacology 2012; 90:125-32. [PMID: 22832366 DOI: 10.1159/000340054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 06/13/2012] [Indexed: 11/19/2022]
Abstract
BACKGROUND Obesity is an increasing burden affecting developed and emerging societies since it is associated with an increased risk of diabetes and consequent cardiovascular complications. Increasing evidence points towards a pivotal role of inflammation in the etiology of vascular dysfunction. Our study aimed to investigate signs of inflammation and their relation to vascular dysfunction in rats receiving a high fat diet. METHODS Diet-induced obese (DIO) rats were used as a model since these rats exhibit a human pre-diabetic pathology. Oral glucose and insulin tolerance tests were conducted on DIO rats and their controls prior to the development of insulin resistance. Furthermore, the plasma contents of selected cytokines [macrophage chemoattractant protein (MCP-1), interleukin-6 (IL-6), and interleukin-1 (IL-1)] and the concentration of adiponectin were measured. Using wire myography, we tested the vascular function of isolated small mesenteric arteries. RESULTS DIO animals had significantly (p < 0.05) increased body weight (721.2 ± 6.3 g) compared to age- and sex-matched controls (643.4 ± 14.6 g), as well as a significant increase (p < 0.01) in body fat percentage (29.7 ± 1.7% and 22.7 ± 0.97%, respectively). No significant difference in fasting plasma insulin levels could be detected between the two groups (chow-fed group 141.5 ± 15.1 pmol/l; high fat-fed group 125.9 ± 18.8 pmol/l). However, the levels of MCP-1 (89.7 ± 4.2 pg/ml vs. 60.8 ± 7.7 pg/ml) and IL-6 (61.6 ± 3.1 pg/ml vs. 41.6 ± 7.4 pg/ml) were significantly elevated in DIO animals (p < 0.05) as compared to controls. Adiponectin levels were also significantly increased (p < 0.01) in DIO rats (10.8 ± 0.7 ng/ml) versus controls (6.9 ± 0.5 ng/ml). No difference in vascular or endothelial function was evident as determined by responses to acetylcholine, sodium nitroprusside, endothelin-1, and calcitonin gene-related peptide. CONCLUSION In DIO rats, which have not yet developed hyperinsulinaemia or glucose intolerance, the levels of inflammatory mediators MCP-1 and Il-6 are significantly increased without concomitant vascular dysfunction. The results show that inflammation and obesity are tightly associated, and that inflammation is manifested prior to significant insulin resistance and vascular dysfunction.
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Affiliation(s)
- Martin Blædel
- Hagedorn Research Institute, Novo Nordisk, Gentofte, Denmark.
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Huang G, Tong C, Kumbhani DS, Ashton C, Yan H, Ying QL. Beyond knockout rats: new insights into finer genome manipulation in rats. Cell Cycle 2011; 10:1059-66. [PMID: 21383544 DOI: 10.4161/cc.10.7.15233] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The ability to "knockout" specific genes in mice via embryonic stem (ES) cell-based gene-targeting technology has significantly enriched our understanding of gene function in normal and disease phenotypes. Improvements on this original strategy have been developed to enable the manipulation of genomes in a more sophisticated fashion with unprecedented precision. The rat is the model of choice in many areas of scientific investigation despite the lack of rat genetic toolboxes. Most Recent advances of zinc finger nucleases (ZFNs) and rat ES cells are diminishing the gap between rat and mouse with respect to reverse genetic approaches. Importantly, the establishment of rat ES cell-based gene targeting technology, in combination with the unique advantages of using rats, provides new, exciting opportunities to create animal models that mimic human diseases more faithfully. We hereby report our recent results concerning finer genetic modifications in the rat, and propose their potential applications in addressing biological questions.
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Affiliation(s)
- Guanyi Huang
- Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
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