The Mouse Genome Database (MGD): mouse biology and model systems

Bult, Carol J.; Eppig, Janan T.; Kadin, James A.; Richardson, Joel E.; Blake, Judith A.

doi:10.1093/nar/gkm961

Cited by 404 publications

(434 citation statements)

References 15 publications

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“…Despite similar names and generally similar hearing characteristics for the first year, these two strains appear to model different forms of presbycusis. The 980 year span over which these strains have diverged (Fox et al 1997) has been ample time for the accumulation of over 2,200 known genetic differences, including at least 41 non-synonymous exonic base changes (Bult et al 2008). These or other polymorphisms must alter qualitatively the trajectory of cochlear aging.…”

Section: Discussionmentioning

confidence: 99%

Divergent Aging Characteristics in CBA/J and CBA/CaJ Mouse Cochleae

Ohlemiller

Dahl

Gagnon

2010

JARO

100

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Two inbred mouse strains, CBA/J and CBA/CaJ, have been used nearly interchangeably as 'good hearing' standards for research in hearing and deafness. We recently reported, however, that these two strains diverge after 1 year of age, such that CBA/CaJ mice show more rapid elevation of compound action potential (CAP) thresholds at high frequencies (Ohlemiller, Brain Res. 1277: 70-83, 2009). One contributor is progressive decline in endocochlear potential (EP) that appears only in CBA/CaJ. Here, we explore the cellular bases of threshold and EP disparities in old CBA/J and CBA/CaJ mice. Among the major findings, both strains exhibit a characteristic age (∼18 months in CBA/J and 24 months in CBA/CaJ) when females overtake males in sensitivity decline. Strain differences in progression of hearing loss are not due to greater hair cell loss in CBA/ CaJ, but instead appear to reflect greater neuronal loss, plus more pronounced changes in the lateral wall, leading to EP decline. While both male and female CBA/CaJ show these pathologies, they are more pronounced in females. A novel feature that differed sharply by strain was moderate loss of outer sulcus cells (or 'root' cells) in spiral ligament of the upper basal turn in old CBA/CaJ mice, giving rise to deep indentations and void spaces in the ligament. We conclude that CBA/CaJ mice differ both quantitatively and qualitatively from CBA/J in age-related cochlear pathology, and model different types of presbycusis.

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Section: Discussionmentioning

confidence: 99%

Divergent Aging Characteristics in CBA/J and CBA/CaJ Mouse Cochleae

Ohlemiller

Dahl

Gagnon

2010

JARO

100

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“…Belly spotting is an easily identifiable trait, and numerous independent mutations have been recovered in breeding colonies as well as in radiation or chemical mutagenesis studies (Bult et al 2008). The fact that none were mapped to this region of Chr 2 would imply that either a mutation at a potential single gene target within this region has not yet been recovered or that a potential single gene target does not exist.…”

Section: Discussionmentioning

confidence: 99%

“…An extensive allelic series at Pax6 has been identified (Bult et al 2008). Heterozygote Pax6 in- /3Neu were submitted to and approved by the Mouse Genetic Nomenclature Committee, and assigned the MGI accession ID nos.…”

mentioning

confidence: 99%

Analysis of Pax6 Contiguous Gene Deletions in the Mouse, Mus musculus, Identifies Regions Distinct from Pax6 Responsible for Extreme Small-Eye and Belly-Spotting Phenotypes

et al. 2009

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In the mouse Pax6 function is critical in a dose-dependent manner for proper eye development. Pax6 contiguous gene deletions were shown to be homozygous lethal at an early embryonic stage. Heterozygotes express belly spotting and extreme microphthalmia. The eye phenotype is more severe than in heterozygous Pax6 intragenic null mutants, raising the possibility that deletions are functionally different from intragenic null mutations or that a region distinct from Pax6 included in the deletions affects eye phenotype. We recovered and identified the exact regions deleted in three new Pax6 deletions. All are homozygous lethal at an early embryonic stage. None express belly spotting. One expresses extreme microphthalmia and two express the milder eye phenotype similar to Pax6 intragenic null mutants. Analysis of Pax6 expression levels and the major isoforms excluded the hypothesis that the deletions expressing extreme microphthalmia are directly due to the action of Pax6 and functionally different from intragenic null mutations. A region distinct from Pax6 containing eight genes was identified for belly spotting. A second region containing one gene (Rcn1) was identified for the extreme microphthalmia phenotype. Rcn1 is a Ca 12 -binding protein, resident in the endoplasmic reticulum, participates in the secretory pathway and expressed in the eye. Our results suggest that deletion of Rcn1 directly or indirectly contributes to the eye phenotype in Pax6 contiguous gene deletions.

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“…In order to support the analysis of the data they obtained, various databases need to be integrated. The immunologists choose to bootstrap a dataspace by including in it the following data sources: Genbank [7], which stores the genetic sequences of a large number or organisms; MGD [13], the Mouse Genome Database; Gene Ontology [63], which is a knowledge base on the function of genes; and KEGG [39], a pathway database that is conjectured to contain relevant information on pathways additional to those in MGD. Figure 10 shows the bootstrapping of this dataspace and is analogous to the example in Fig.…”

Section: A Bioinformatics Use Casementioning

confidence: 99%

A Functional Model for Dataspace Management Systems

Hedeler

Fernandes

Belhajjame

et al. 2013

Advanced Query Processing

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Dataspace management systems (DSMSs) hold the promise of pay-asyou-go data integration. We describe a comprehensive model of DSMS functionality using an algebraic style. We begin by characterizing a dataspace life cycle and highlighting opportunities for both automation and user-driven improvement techniques. Building on the observation that many of the techniques developed in model management are of use in data integration contexts as well, we briefly introduce the model management area and explain how previous work on both data integration and model management needs extending if the full dataspace life cycle is to be supported. We show that many model management operators already enable important functionality (e.g., the merging of schemas, the composition of mappings, etc.) and formulate these capabilities in an algebraic structure, thereby giving rise to the notion of the core functionality of a DSMS as a many-sorted algebra. Given this view, we show how core tasks in the dataspace life cycle can be enacted by means of algebraic programs. An extended case study illustrates how such algebraic programs capture a challenging, practical scenario.

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The Mouse Genome Database (MGD): mouse biology and model systems

Cited by 404 publications

References 15 publications

Divergent Aging Characteristics in CBA/J and CBA/CaJ Mouse Cochleae

Divergent Aging Characteristics in CBA/J and CBA/CaJ Mouse Cochleae

Analysis of Pax6 Contiguous Gene Deletions in the Mouse, Mus musculus, Identifies Regions Distinct from Pax6 Responsible for Extreme Small-Eye and Belly-Spotting Phenotypes

A Functional Model for Dataspace Management Systems

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