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The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes

Charles A. Steward, Jose M. Gonzalez, Steve Trevanion, Dan Sheppard, Giselle Kerry, James G. R. Gilbert, Linda S. Wicker, Jane Rogers, Jennifer L. Harrow
2013 Database: The Journal of Biological Databases and Curation  
The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes.  ...  The non-obese diabetic (NOD) mouse is an experimental model for T1D having been bred to develop the disease spontaneously in a process that is similar to humans.  ...  Acknowledgements The authors thank Thomas Keane for his advice and help with the variation calling and the teams in mapping, sequence production, finishing, annotation and analysis for their contributions  ... 
doi:10.1093/database/bat032 pmid:23729657 pmcid:PMC3668384 fatcat:erziwmzbzbhyld255qmq5xgvkm

Rat Genome and Model Resources

Mary Shimoyama, Jennifer R. Smith, Elizabeth Bryda, Takashi Kuramoto, Laura Saba, Melinda Dwinell
2017 ILAR journal  
Advanced sequencing technologies, genome modification techniques, and the development of embryonic stem cell protocols ensure the rat remains an important mammalian model for disease studies.  ...  Those profiled here include the Rat Genome Database, PhenoGen, Gene Editing Rat Resource Center, Rat Resource and Research Center, and the National BioResource Project for the Rat in Japan.  ...  Department of Health and Human Services, National Institutes of Health, NIH Office of the Director, grant #P40OD011062 (RRRC); and the Ministry of Education, Culture, Sports, Science and Technology (MEXT  ... 
doi:10.1093/ilar/ilw041 pmid:28838068 pmcid:PMC6057551 fatcat:35ugntkgzzc6jl3o546n7cidhy

[Management, Ethics, Welfare] [Microbiology, Infection, Immunity] [Disease Models] [Bio-Resources] [Methodology, Replacement, Refinement] [Senescence] [Neuroscience, Behavior] [Reproduction] [Embryo Manipulation, Regenerative Medicine] [Genetics, Breeding, Gene Functions]

2016 Experimental animals  
This facility used disposable mouse cages and therefore a usual large autoclave was not necessary.  ...  Therefore the fecal pH changes of mice are a useful indicator of stress exposure that may be determined by a simple, rapid, and non-invasive manner. -S 73-P-9  ...  P-100 Identification of the responsible gene for Stmm1a by congenic mapping and gene expression analysis ○Kazuhiro Okumura 1,2 , Megumi Saito 2 , Yasuhiro Yoshizawa 2 , Eriko Isogai 2 , Ikuo Miura 3 ,  ... 
doi:10.1538/expanim.65suppl-p pmid:27374810 pmcid:PMC5338225 fatcat:dihzqzslszai3prcphnpelzoy4

White adipose tissue reference network: a knowledge resource for exploring health-relevant relations

Thomas Kelder, Georg Summer, Martien Caspers, Evert M. van Schothorst, Jaap Keijer, Loes Duivenvoorde, Susanne Klaus, Anja Voigt, Laura Bohnert, Catalina Pico, Andreu Palou, M. Luisa Bonet (+9 others)
2014 Genes & Nutrition  
We have validated the reference network by showing overrepresentation with anti-obesity drug targets, pathology-associated genes and differentially expressed genes from an external disease model dataset  ...  Following this principle, five anti-diabetic drug interventions and one diet intervention were scored for the match of their expression signature to the five biomarker signatures derived from the WATRefNet  ...  Acknowledgments We thank Francesc Puiggros for his contribution to definition of relevant physiological processes determining WAT health status, critical assessment of the manuscript and support of collaboration  ... 
doi:10.1007/s12263-014-0439-x pmid:25466819 pmcid:PMC4252261 fatcat:exty7v2otrf27m4dc5ouebfqoi

Disease, Models, Variants and Altered Pathways—Journeying RGD Through the Magnifying Glass

Victoria Petri, G. Thomas Hayman, Marek Tutaj, Jennifer R. Smith, Stan Laulederkind, Shur-Jen Wang, Rajni Nigam, Jeff De Pons, Mary Shimoyama, Melinda R. Dwinell
2016 Computational and Structural Biotechnology Journal  
From many entry points, data can be accessed and results retrieved. To illustrate, diabetes is used as a case study to initiate and embark upon an exploratory journey.  ...  The vocabularies/ontologies allow the capture of disease and phenotype associations of rat strains and QTLs, as well as disease and pathway associations of rat, human and mouse genes.  ...  Acknowledgments The RGD project is funded by Grant HL064541 from the National Heart, Lung, and Blood Institute on behalf of the National Institutes of Health.  ... 
doi:10.1016/j.csbj.2015.11.006 pmid:27602200 pmcid:PMC4700298 fatcat:mtz3rsiqp5esxf6qbfgygrzgyy

Phenotype Data: A Neglected Resource in Biomedical Research?

Philip Groth, Bertram Weiss
2006 Current Bioinformatics  
In light of these developments, we thoroughly surveyed the available phenotype resources and reviewed different approaches to analyzing their content.  ...  We discuss hurdles yet to be overcome, i.e. the lack of data integration, the missing adequate phenotype ontologies and the shortage of appropriate analytical tools.  ...  ACKNOWLEDGEMENTS We are grateful to Bernard Haendler (Schering AG) for useful discussions of the manuscript and to the referee's valuable comments and suggestions.  ... 
doi:10.2174/157489306777828008 fatcat:kkgtcwoluzc7xlt7uwpp5k7zyu

The Collaborative Cross: A Systems Genetics Resource for Studying Host-Pathogen Interactions

Kelsey E. Noll, Martin T. Ferris, Mark T. Heise
2019 Cell Host and Microbe  
The study of pathogen resistance genes, largely aided by mouse models, has significantly advanced our understanding of infectious disease pathogenesis.  ...  In this review, we summarize progress utilizing the CC as a platform to develop improved models of pathogen-induced disease and to map polymorphic host response loci associated with variation in susceptibility  ...  ACKNOWLEDGMENTS We would like to thank Sharon Taft-Benz, Sanjay Sarkar, Emily Madden, and Brea Hampton for critical reading of the manuscript.  ... 
doi:10.1016/j.chom.2019.03.009 pmid:30974083 pmcid:PMC6494101 fatcat:x3ujt2j3dnfr7b2f5w3yby772m

Common and Rare Genetic Variation inCCR2,CCR5, orCX3CR1and Risk of Atherosclerotic Coronary Heart Disease and Glucometabolic TraitsCLINICAL PERSPECTIVE

Jessica R. Golbus, Nathan O. Stitziel, Wei Zhao, Chenyi Xue, Martin Farrall, Ruth McPherson, Jeanette Erdmann, Panos Deloukas, Hugh Watkins, Heribert Schunkert, Nilesh J. Samani, Danish Saleheen (+2 others)
2016 Circulation: Cardiovascular Genetics  
Acknowledgments We acknowledge outstanding support from colleagues in the Sources of Funding Disclosures None.  ...  The predicted functional impact of each rare variant was annotated using 7 algorithms, [25] [26] [27] [28] [29] [30] and we tested for an association separately for 3 classes of variants: (1) nonsynonymous  ...  The PROMIS MI resource is described above. 17, 18 In addition to MI, association tests were performed for type II DM and lipid levels (Table 1) , and summary data extracted for SNPs within 5000 bps  ... 
doi:10.1161/circgenetics.115.001374 pmid:27013693 pmcid:PMC5015681 fatcat:n7pvfcfvd5ep7mpwwtdg32dkim

A systems genetics resource and analysis of sleep regulation in the mouse

Shanaz Diessler, Maxime Jan, Yann Emmenegger, Nicolas Guex, Benita Middleton, Debra J. Skene, Mark Ibberson, Frederic Burdet, Lou Götz, Marco Pagni, Martial Sankar, Robin Liechti (+4 others)
2018 PLoS Biology  
The resource, together with an interactive interface for datamining, can be found under and is maintained by the SIB (Swiss Institute for Bioinformatics).  ...  OPEN ACCESS Citation: Diessler S, Jan M, Emmenegger Y, Guex N, Middleton B, Skene DJ, et al. (2018) A systems genetics resource and analysis of sleep regulation in the mouse.  ...  Cohen for sharing the Acot11 KO mice; Derk-Jan Dijk for detailed and critical comments, which helped improve the manuscript; and to Judith Zaugg and Bernard Thorens for insightful discussion.  ... 
doi:10.1371/journal.pbio.2005750 pmid:30091978 pmcid:PMC6085075 fatcat:sgxwd56u4vdtbealozivarfona

Genetics of Type 1 Diabetes: What's Next?

F. Pociot, B. Akolkar, P. Concannon, H. A. Erlich, C. Julier, G. Morahan, C. R. Nierras, J. A. Todd, S. S. Rich, J. Nerup
2010 Diabetes  
resources for type 1 diabetes research (1) .  ...  The International Type 1 Diabetes Genetics Consortium (T1DGC) has established significant resources for the study of genetics of type 1 diabetes.  ... 
doi:10.2337/db10-0076 pmid:20587799 pmcid:PMC2889752 fatcat:nixvp6qw45hchkp3bszzklsuzq

Genome-wide interrogation reveals hundreds of long intergenic noncoding RNAs that associate with cardiometabolic traits

Rachel L. Ballantyne, Xuan Zhang, Sara Nuñez, Chenyi Xue, Wei Zhao, Eric Reed, Danish Salaheen, Andrea S. Foulkes, Mingyao Li, Muredach P. Reilly
2016 Human Molecular Genetics  
For trait-associated lincRNAs, we also investigated synteny and conservation relative to mouse, expression patterns in five cardiometabolic-relevant tissues, and allele-specific expression in RNA sequencing  ...  Finally, we revealed a functional role in human adipocytes for linc-NFE2L3-1, which is expressed in adipose and is associated with waist-hip ratio adjusted for BMI.  ...  Data on LDL-C, HDL-C, triglycerides and total cholesterol have been contributed by GLGC, the Global Lipids Genetics Consortium  ... 
doi:10.1093/hmg/ddw154 pmid:27288454 pmcid:PMC5181595 fatcat:r3cbeok5ubah5ppwrh6hao2qai

Advances in comparative genetics: influence of genetics on obesity

Wendy Foulds Mathes, Scott A. Kelly, Daniel Pomp
2011 British Journal of Nutrition  
We consider the evolution of mouse models into more informative resources such as outbred crosses and the Hybrid Mouse Diversity Panel, as well as novel next-generation approaches such as the Collaborative  ...  In the present review, we survey past use and examine new advances in mouse models designed to uncover the genetic architecture of obesity and its component traits.  ...  Acknowledgements Sections of the present review were supported by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) (grants no. RC1DK087346 and no. DK076050).  ... 
doi:10.1017/s0007114511001905 pmid:22005399 fatcat:ahwkjd3lj5fopdhoucyf6u3uqu

T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders

Jyoti Rani, Inna Mittal, Atreyi Pramanik, Namita Singh, Namita Dube, Smriti Sharma, Bhanwar Lal Puniya, Muthukurussi Varieth Raghunandanan, Ahmed Mobeen, Srinivasan Ramachandran
2017 Scientific Reports  
We performed integrative analysis of genes associated with type 2 Diabetes Mellitus (T2DM) associated complications by automated text mining with manual curation and also gene expression analysis from  ...  T2DM is on the rise 1 . It is characterized by hyperglycaemia due to insulin resistance and decreased insulin activity.  ...  Acknowledgements We thank Ms Priyanka Shrivastava and Ms Anasuya Bhargava for useful feedback. This work was supported by Council of Scientific and Industrial Research through grant BSC0122.  ... 
doi:10.1038/s41598-017-07238-0 pmid:28761062 pmcid:PMC5537262 fatcat:nk4272yk3jg43hhbgb5wje4d7q

Gene expression profiling in islet biology and diabetes research

Ernesto Bernal-Mizrachi, Corentin Cras-Méneur, Mitsuru Ohsugi, M. Alan Permutt
2002 Diabetes/Metabolism Research Reviews  
This protein has been proposed to be a target of the autoimmune response in the Non-Obese Diabetic (NOD) mouse [14].  ...  type 1 diabetes.  ... 
doi:10.1002/dmrr.331 pmid:12592642 fatcat:7pdpzquuvvf25fi52szhcxhd5q

Genome Editing Human Pluripotent Stem Cells to Model β-Cell Disease and Unmask Novel Genetic Modifiers

Matthew N. George, Karla F. Leavens, Paul Gadue
2021 Frontiers in Endocrinology  
Here we review the contribution of protein coding and non-protein coding genetic disease modifiers to the pathogenesis of diabetes subtypes, as well as how recent technological advances in the generation  ...  A mechanistic understanding of the genetic basis of complex diseases such as diabetes mellitus remain elusive due in large part to the activity of genetic disease modifiers that impact the penetrance and  ...  As a result, diabetes manifests differently in the two species: for example, the commonly-used non-obese diabetic (NOD) mouse strain exhibits pronounced insulitis and rapid b-cell destruction, while b-cell  ... 
doi:10.3389/fendo.2021.682625 pmid:34149620 pmcid:PMC8206553 fatcat:5kwfhsowdjcrngkq2mpbfmm3sm
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