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McIlwrath SL, Starr ME, High AE, Saito H, Westlund KN. Effect of acetyl-L-carnitine on hypersensitivity in acute recurrent caerulein-induced pancreatitis and microglial activation along the brain’s pain circuitry. World J Gastroenterol 2021; 27:794-814. [PMID: 33727771 PMCID: PMC7941858 DOI: 10.3748/wjg.v27.i9.794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/08/2020] [Accepted: 01/15/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Acute pancreatitis (AP) and recurring AP are serious health care problems causing excruciating pain and potentially lethal outcomes due to sepsis. The validated caerulein- (CAE) induced mouse model of acute/recurring AP produces secondary persistent hypersensitivity and anxiety-like behavioral changes for study.
AIM To determine efficacy of acetyl-L-carnitine (ALC) to reduce pain-related behaviors and brain microglial activation along the pain circuitry in CAE-pancreatitis.
METHODS Pancreatitis was induced with 6 hly intraperitoneal (i.p.) injections of CAE (50 µg/kg), 3 d a week for 6 wk in male C57BL/6J mice. Starting in week 4, mice received either vehicle or ALC until experiment’s end. Mechanical hyper-sensitivity was assessed with von Frey filaments. Heat hypersensitivity was determined with the hotplate test. Anxiety-like behavior was tested in week 6 using elevated plus maze and open field tests. Microglial activation in brain was quantified histologically by immunostaining for ionized calcium-binding adaptor molecule 1 (Iba1).
RESULTS Mice with CAE-induced pancreatitis had significantly reduced mechanical withdrawal thresholds and heat response latencies, indicating ongoing pain. Treatment with ALC attenuated inflammation-induced hypersensitivity, but hypersensitivity due to abdominal wall injury caused by repeated intraperitoneal injections persisted. Animals with pancreatitis displayed spontaneous anxiety-like behavior in the elevated plus maze compared to controls. Treatment with ALC resulted in increased numbers of rearing activity events, but time spent in “safety” was not changed. After all the abdominal injections, pancreata were translucent if excised at experiment’s end and opaque if excised on the subsequent day, indicative of spontaneous healing. Post mortem histopathological analysis performed on pancreas sections stained with Sirius Red and Fast Green identified wide-spread fibrosis and acinar cell atrophy in sections from mice with CAE-induced pancreatitis that was not rescued by treatment with ALC. Microglial Iba1 immunostaining was significantly increased in hippocampus, thalamus (intralaminar nuclei), hypothalamus, and amygdala of mice with CAE-induced pancreatitis compared to naïve controls but unchanged in the primary somatosensory cortex compared to naïves.
CONCLUSION CAE-induced pancreatitis caused increased pain-related behaviors, pancreatic fibrosis, and brain microglial changes. ALC alleviated CAE-induced mechanical and heat hypersensitivity but not abdominal wall injury-induced hypersensitivity caused by the repeated injections.
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Affiliation(s)
- Sabrina L McIlwrath
- Research Service, New Mexico Veterans Affairs Healthcare System, Albuquerque, NM 87108, United States
| | - Marlene E Starr
- Department of Surgery, University of Kentucky, Lexington, KY 40536, United States
| | - Abigail E High
- College of Liberal Arts, University of Texas, Austin, TX 78712, United States
| | - Hiroshi Saito
- Department of Surgery, University of Kentucky, Lexington, KY 40536, United States
| | - Karin N Westlund
- Research Service, New Mexico Veterans Affairs Healthcare System, Albuquerque, NM 87108, United States
- Department of Anesthesiology and Critical Care Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, United States
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Shrivastava AN, Redeker V, Pieri L, Bousset L, Renner M, Madiona K, Mailhes-Hamon C, Coens A, Buée L, Hantraye P, Triller A, Melki R. Clustering of Tau fibrils impairs the synaptic composition of α3-Na +/K +-ATPase and AMPA receptors. EMBO J 2019; 38:embj.201899871. [PMID: 30630857 PMCID: PMC6356061 DOI: 10.15252/embj.201899871] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 01/13/2023] Open
Abstract
Tau assemblies have prion‐like properties: they propagate from one neuron to another and amplify by seeding the aggregation of endogenous Tau. Although key in prion‐like propagation, the binding of exogenous Tau assemblies to the plasma membrane of naïve neurons is not understood. We report that fibrillar Tau forms clusters at the plasma membrane following lateral diffusion. We found that the fibrils interact with the Na+/K+‐ATPase (NKA) and AMPA receptors. The consequence of the clustering is a reduction in the amount of α3‐NKA and an increase in the amount of GluA2‐AMPA receptor at synapses. Furthermore, fibrillar Tau destabilizes functional NKA complexes. Tau and α‐synuclein aggregates often co‐exist in patients’ brains. We now show evidences for cross‐talk between these pathogenic aggregates with α‐synuclein fibrils dramatically enhancing fibrillar Tau clustering and synaptic localization. Our results suggest that fibrillar α‐synuclein and Tau cross‐talk at the plasma membrane imbalance neuronal homeostasis.
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Affiliation(s)
- Amulya Nidhi Shrivastava
- CEA, Institut François Jacob (MIRcen) and CNRS Laboratory of Neurodegenerative Diseases (UMR9199), Fontenay-aux-Roses, France.,Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, INSERM, CNRS, PSL Research University, Paris, France
| | - Virginie Redeker
- CEA, Institut François Jacob (MIRcen) and CNRS Laboratory of Neurodegenerative Diseases (UMR9199), Fontenay-aux-Roses, France
| | - Laura Pieri
- CEA, Institut François Jacob (MIRcen) and CNRS Laboratory of Neurodegenerative Diseases (UMR9199), Fontenay-aux-Roses, France
| | - Luc Bousset
- CEA, Institut François Jacob (MIRcen) and CNRS Laboratory of Neurodegenerative Diseases (UMR9199), Fontenay-aux-Roses, France
| | - Marianne Renner
- INSERM, UMR - S 839 Institut du Fer à Moulin (IFM), Sorbonne Université, Paris, France
| | - Karine Madiona
- CEA, Institut François Jacob (MIRcen) and CNRS Laboratory of Neurodegenerative Diseases (UMR9199), Fontenay-aux-Roses, France
| | - Caroline Mailhes-Hamon
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, INSERM, CNRS, PSL Research University, Paris, France
| | - Audrey Coens
- CEA, Institut François Jacob (MIRcen) and CNRS Laboratory of Neurodegenerative Diseases (UMR9199), Fontenay-aux-Roses, France
| | - Luc Buée
- CHU Lille, INSERM UMR-S 1172 JPArc "Alzheimer & Tauopathies" Universite Lille, Lille, France
| | - Philippe Hantraye
- CEA, Institut François Jacob (MIRcen) and CNRS Laboratory of Neurodegenerative Diseases (UMR9199), Fontenay-aux-Roses, France
| | - Antoine Triller
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, INSERM, CNRS, PSL Research University, Paris, France
| | - Ronald Melki
- CEA, Institut François Jacob (MIRcen) and CNRS Laboratory of Neurodegenerative Diseases (UMR9199), Fontenay-aux-Roses, France
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Abstract
Intraocular pressure (IOP) is the primary risk factor for developing glaucoma, yet little is known about the contribution of genomic background to IOP regulation. The present study leverages an array of systems genetics tools to study genomic factors modulating normal IOP in the mouse. The BXD recombinant inbred (RI) strain set was used to identify genomic loci modulating IOP. We measured the IOP in a total of 506 eyes from 38 different strains. Strain averages were subjected to conventional quantitative trait analysis by means of composite interval mapping. Candidate genes were defined, and immunohistochemistry and quantitative PCR (qPCR) were used for validation. Of the 38 BXD strains examined the mean IOP ranged from a low of 13.2mmHg to a high of 17.1mmHg. The means for each strain were used to calculate a genome wide interval map. One significant quantitative trait locus (QTL) was found on Chr.8 (96 to 103 Mb). Within this 7 Mb region only 4 annotated genes were found: Gm15679, Cdh8, Cdh11 and Gm8730. Only two genes (Cdh8 and Cdh11) were candidates for modulating IOP based on the presence of non-synonymous SNPs. Further examination using SIFT (Sorting Intolerant From Tolerant) analysis revealed that the SNPs in Cdh8 (Cadherin 8) were predicted to not change protein function; while the SNPs in Cdh11 (Cadherin 11) would not be tolerated, affecting protein function. Furthermore, immunohistochemistry demonstrated that CDH11 is expressed in the trabecular meshwork of the mouse. We have examined the genomic regulation of IOP in the BXD RI strain set and found one significant QTL on Chr. 8. Within this QTL, there is one good candidate gene, Cdh11.
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Abstract
PURPOSE This paper presents a deformable mouse atlas of the laboratory mouse anatomy. This atlas is fully articulated and can be positioned into arbitrary body poses. The atlas can also adapt body weight by changing body length and fat amount. PROCEDURES A training set of 103 micro-CT images was used to construct the atlas. A cage-based deformation method was applied to realize the articulated pose change. The weight-related body deformation was learned from the training set using a linear regression method. A conditional Gaussian model and thin-plate spline mapping were used to deform the internal organs following the changes of pose and weight. RESULTS The atlas was deformed into different body poses and weights, and the deformation results were more realistic compared to the results achieved with other mouse atlases. The organ weights of this atlas matched well with the measurements of real mouse organ weights. This atlas can also be converted into voxelized images with labeled organs, pseudo CT images and tetrahedral mesh for phantom studies. CONCLUSIONS With the unique ability of articulated pose and weight changes, the deformable laboratory mouse atlas can become a valuable tool for preclinical image analysis.
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Spontaneous malformations of the cerebellar vermis: Prevalence, inheritance, and relationship to lobule/fissure organization in the C57BL/6 lineage. Neuroscience 2015; 310:242-51. [PMID: 26383253 DOI: 10.1016/j.neuroscience.2015.09.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/09/2015] [Indexed: 11/22/2022]
Abstract
The complex neuronal circuitry of the cerebellum is embedded within its lamina, folia, and lobules, which together play an important role in sensory and motor function. Studies in mouse models have demonstrated that both cerebellar lamination and lobule/fissure development are under genetic control. The cerebellar vermis of C57BL/6 mice exhibits spontaneous malformations of neuronal migration of posterior lobules (VIII-IX; molecular layer heterotopia); however, the extent to which other inbred mice also exhibit these malformations is unknown. Using seven different inbred mouse strains and two first filial generation (F1) hybrids, we show that only the C57BL/6 strain exhibits heterotopia. Furthermore, we observed heterotopia in consomic and recombinant inbred strains. These data indicate that heterotopia formation is a weakly penetrant trait requiring homozygosity of one or more C57BL/6 alleles outside of chromosome 1 and the sex chromosomes. Additional morphological analyses showed no relationship between heterotopia formation and other features of lobule/fissure organization. These data are relevant toward understanding normal cerebellar development and disorders affecting cerebellar foliation and lamination.
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Progressive dopaminergic cell loss with unilateral-to-bilateral progression in a genetic model of Parkinson disease. Proc Natl Acad Sci U S A 2012; 109:15918-23. [PMID: 23019375 DOI: 10.1073/pnas.1205102109] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
DJ-1 mutations cause autosomal recessive early-onset Parkinson disease (PD). We report a model of PD pathology: the DJ1-C57 mouse. A subset of DJ-1-nullizygous mice, when fully backcrossed to a C57BL/6 [corrected] background, display dramatic early-onset unilateral loss of dopaminergic (DA) neurons in their substantia nigra pars compacta, progressing to bilateral degeneration of the nigrostriatal axis with aging. In addition, these mice exhibit age-dependent bilateral degeneration at the locus ceruleus nucleus and display mild motor behavior deficits at aged time points. These findings effectively recapitulate the early stages of PD. Therefore, the DJ1-C57 mouse provides a tool to study the preclinical aspects of neurodegeneration. Importantly, by exome sequencing, we identify candidate modifying genes that segregate with the phenotype, providing potentially critical clues into how certain genes may influence the penetrance of DJ-1-related degeneration in mice.
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Newbury AJ, Rosen GD. Genetic, morphometric, and behavioral factors linked to the midsagittal area of the corpus callosum. Front Genet 2012; 3:91. [PMID: 22666227 PMCID: PMC3364465 DOI: 10.3389/fgene.2012.00091] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 05/07/2012] [Indexed: 12/23/2022] Open
Abstract
The corpus callosum is the main commissure connecting left and right cerebral hemispheres, and varies widely in size. Differences in the midsagittal area of the corpus callosum (MSACC) have been associated with a number of cognitive and behavioral phenotypes, including obsessive-compulsive disorders, psychopathy, suicidal tendencies, bipolar disorder, schizophrenia, autism, and attention deficit hyperactivity disorder. Although there is evidence to suggest that MSACC is heritable in normal human populations, there is surprisingly little evidence concerning the genetic modulation of this variation. Mice provide a potentially ideal tool to dissect the genetic modulation of MSACC. Here, we use a large genetic reference panel – the BXD recombinant inbred line – to dissect the natural variation of the MSACC. We estimated the MSACC in over 300 individuals from nearly 80 strains. We found a 4-fold difference in MSACC between individual mice, and a 2.5-fold difference among strains. MSACC is a highly heritable trait (h2 = 0.60), and we mapped a suggestive QTL to the distal portion of Chr 14. Using sequence data and neocortical expression databases, we were able to identify eight positional and plausible biological candidate genes within this interval. Finally, we found that MSACC correlated with behavioral traits associated with anxiety and attention.
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Affiliation(s)
- Alex J Newbury
- Department of Neurology, Beth Israel Deaconess Medical Center Boston, MA, USA
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Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2012. [PMID: 23195313 DOI: 10.1016/b978-0-12-398323-7.00005-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Postgenomic studies of the function of genes and their role in disease have now become an area of intense study since efforts to define the raw sequence material of the genome have largely been completed. The use of whole-genome approaches such as microarray expression profiling and, more recently, RNA-sequence analysis of transcript abundance has allowed an unprecedented look at the workings of the genome. However, the accurate derivation of such high-throughput data and their analysis in terms of biological function has been critical to truly leveraging the postgenomic revolution. This chapter will describe an approach that focuses on the use of gene networks to both organize and interpret genomic expression data. Such networks, derived from statistical analysis of large genomic datasets and the application of multiple bioinformatics data resources, potentially allow the identification of key control elements for networks associated with human disease, and thus may lead to derivation of novel therapeutic approaches. However, as discussed in this chapter, the leveraging of such networks cannot occur without a thorough understanding of the technical and statistical factors influencing the derivation of genomic expression data. Thus, while the catch phrase may be "it's the network … stupid," the understanding of factors extending from RNA isolation to genomic profiling technique, multivariate statistics, and bioinformatics are all critical to defining fully useful gene networks for study of complex biology.
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Bottomly D, Walter NAR, Hunter JE, Darakjian P, Kawane S, Buck KJ, Searles RP, Mooney M, McWeeney SK, Hitzemann R. Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays. PLoS One 2011; 6:e17820. [PMID: 21455293 PMCID: PMC3063777 DOI: 10.1371/journal.pone.0017820] [Citation(s) in RCA: 177] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 02/10/2011] [Indexed: 12/14/2022] Open
Abstract
C57BL/6J (B6) and DBA/2J (D2) are two of the most commonly used inbred mouse strains in neuroscience research. However, the only currently available mouse genome is based entirely on the B6 strain sequence. Subsequently, oligonucleotide microarray probes are based solely on this B6 reference sequence, making their application for gene expression profiling comparisons across mouse strains dubious due to their allelic sequence differences, including single nucleotide polymorphisms (SNPs). The emergence of next-generation sequencing (NGS) and the RNA-Seq application provides a clear alternative to oligonucleotide arrays for detecting differential gene expression without the problems inherent to hybridization-based technologies. Using RNA-Seq, an average of 22 million short sequencing reads were generated per sample for 21 samples (10 B6 and 11 D2), and these reads were aligned to the mouse reference genome, allowing 16,183 Ensembl genes to be queried in striatum for both strains. To determine differential expression, ‘digital mRNA counting’ is applied based on reads that map to exons. The current study compares RNA-Seq (Illumina GA IIx) with two microarray platforms (Illumina MouseRef-8 v2.0 and Affymetrix MOE 430 2.0) to detect differential striatal gene expression between the B6 and D2 inbred mouse strains. We show that by using stringent data processing requirements differential expression as determined by RNA-Seq is concordant with both the Affymetrix and Illumina platforms in more instances than it is concordant with only a single platform, and that instances of discordance with respect to direction of fold change were rare. Finally, we show that additional information is gained from RNA-Seq compared to hybridization-based techniques as RNA-Seq detects more genes than either microarray platform. The majority of genes differentially expressed in RNA-Seq were only detected as present in RNA-Seq, which is important for studies with smaller effect sizes where the sensitivity of hybridization-based techniques could bias interpretation.
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Affiliation(s)
- Daniel Bottomly
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, Oregon, United States of America.
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SynapticDB, effective web-based management and sharing of data from serial section electron microscopy. Neuroinformatics 2010; 9:39-57. [PMID: 21181305 PMCID: PMC3063557 DOI: 10.1007/s12021-010-9088-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Serial section electron microscopy (ssEM) is rapidly expanding as a primary tool to investigate synaptic circuitry and plasticity. The ultrastructural images collected through ssEM are content rich and their comprehensive analysis is beyond the capacity of an individual laboratory. Hence, sharing ultrastructural data is becoming crucial to visualize, analyze, and discover the structural basis of synaptic circuitry and function in the brain. We devised a web-based management system called SynapticDB (http://synapses.clm.utexas.edu/synapticdb/) that catalogues, extracts, analyzes, and shares experimental data from ssEM. The management strategy involves a library with check-in, checkout and experimental tracking mechanisms. We developed a series of spreadsheet templates (MS Excel, Open Office spreadsheet, etc) that guide users in methods of data collection, structural identification, and quantitative analysis through ssEM. SynapticDB provides flexible access to complete templates, or to individual columns with instructional headers that can be selected to create user-defined templates. New templates can also be generated and uploaded. Research progress is tracked via experimental note management and dynamic PDF forms that allow new investigators to follow standard protocols and experienced researchers to expand the range of data collected and shared. The combined use of templates and tracking notes ensures that the supporting experimental information is populated into the database and associated with the appropriate ssEM images and analyses. We anticipate that SynapticDB will serve future meta-analyses towards new discoveries about the composition and circuitry of neurons and glia, and new understanding about structural plasticity during development, behavior, learning, memory, and neuropathology.
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MBAT: a scalable informatics system for unifying digital atlasing workflows. BMC Bioinformatics 2010; 11:608. [PMID: 21176225 PMCID: PMC3023809 DOI: 10.1186/1471-2105-11-608] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 12/22/2010] [Indexed: 11/10/2022] Open
Abstract
Background Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data. Results The MouseBIRN Atlasing Toolkit (MBAT) project was developed as a cross-platform, free open-source application that unifies and accelerates the digital atlas workflow. A tiered, plug-in architecture was designed for the neuroinformatics and genomics goals of the project to provide a modular and extensible design. MBAT provides the ability to use a single query to search and retrieve data from multiple data sources, align image data using the user's preferred registration method, composite data from multiple sources in a common space, and link relevant informatics information to the current view of the data or atlas. The workspaces leverage tool plug-ins to extend and allow future extensions of the basic workspace functionality. A wide variety of tool plug-ins were developed that integrate pre-existing as well as newly created technology into each workspace. Novel atlasing features were also developed, such as supporting multiple label sets, dynamic selection and grouping of labels, and synchronized, context-driven display of ontological data. Conclusions MBAT empowers researchers to discover correlations among disparate data by providing a unified environment for bringing together distributed reference resources, a user's image data, and biological atlases into the same spatial or semantic context. Through its extensible tiered plug-in architecture, MBAT allows researchers to customize all platform components to quickly achieve personalized workflows.
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Heydel JM, Holsztynska EJ, Legendre A, Thiebaud N, Artur Y, Le Bon AM. UDP-glucuronosyltransferases (UGTs) in neuro-olfactory tissues: expression, regulation, and function. Drug Metab Rev 2010; 42:74-97. [PMID: 20067364 DOI: 10.3109/03602530903208363] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This work aims to review uridine diphosphate (UDP)-glucuronosyltransferase (UGT) expression and activities along different neuronal structures involved in the common physiological process of olfaction: olfactory epithelium, olfactory bulb, and olfactory cortex. For the first time, using high-throughput in situ hybridization data generated by the Allen Brain Atlas (ABA), we present quantitative analysis of spatial distribution of UGT genes in the mouse brain. The olfactory area is a central nervous system site with the highest expression of UGTs, including UGT isoforms not previously identified in the brain. Since there is evidence of the transfer of xenobiotics to the brain through the nasal pathway, circumventing the blood-brain barrier, olfactory UGTs doubtlessly share the common function of detoxification, but they are also involved in the metabolism and turnover of exogenous or endogenous compounds critical for physiological olfactory processing in these tissues. The function of olfactory UGTs will be discussed with a special focus on their participation in the perireceptor events involved in the modulation of olfactory perception.
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Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ. High-throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains. GENES, BRAIN, AND BEHAVIOR 2010; 9:129-59. [PMID: 19958391 PMCID: PMC2855868 DOI: 10.1111/j.1601-183x.2009.00540.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 08/14/2009] [Accepted: 09/09/2009] [Indexed: 01/10/2023]
Abstract
Genetic reference populations, particularly the BXD recombinant inbred (BXD RI) strains derived from C57BL/6J and DBA/2J mice, are a valuable resource for the discovery of the bio-molecular substrates and genetic drivers responsible for trait variation and covariation. This approach can be profitably applied in the analysis of susceptibility and mechanisms of drug and alcohol use disorders for which many predisposing behaviors may predict the occurrence and manifestation of increased preference for these substances. Many of these traits are modeled by common mouse behavioral assays, facilitating the detection of patterns and sources of genetic coregulation of predisposing phenotypes and substance consumption. Members of the Tennessee Mouse Genome Consortium (TMGC) have obtained phenotype data from over 250 measures related to multiple behavioral assays across several batteries: response to, and withdrawal from cocaine, 3,4-methylenedioxymethamphetamine; "ecstasy" (MDMA), morphine and alcohol; novelty seeking; behavioral despair and related neurological phenomena; pain sensitivity; stress sensitivity; anxiety; hyperactivity and sleep/wake cycles. All traits have been measured in both sexes in approximately 70 strains of the recently expanded panel of BXD RI strains. Sex differences and heritability estimates were obtained for each trait, and a comparison of early (N = 32) and recent (N = 37) BXD RI lines was performed. Primary data are publicly available for heritability, sex difference and genetic analyses using the MouseTrack database, and are also available in GeneNetwork.org for quantitative trait locus (QTL) detection and genetic analysis of gene expression. Together with the results of related studies, these data form a public resource for integrative systems genetic analysis of neurobehavioral traits.
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Affiliation(s)
- V M Philip
- Systems Genetics Group, Biosciences Division, Oak Ridge National LaboratoryOak Ridge TN
| | - S Duvvuru
- Systems Genetics Group, Biosciences Division, Oak Ridge National LaboratoryOak Ridge TN
| | - B Gomero
- Systems Genetics Group, Biosciences Division, Oak Ridge National LaboratoryOak Ridge TN
| | - T A Ansah
- Department of Neurobiology and Neurotoxicology, Meharry Medical CollegeNashville, TN
| | - C D Blaha
- Department of Psychology, The University of MemphisMemphis, TN
| | - M N Cook
- Department of Psychology, The University of MemphisMemphis, TN
| | - K M Hamre
- Departments of Anatomy and Neurobiology, University of Tennessee Health Science CenterMemphis, TN
| | - W R Lariviere
- Departments of Anesthesiology and Neurobiology, University of Pittsburgh School of MedicinePittsburgh, PA
| | - D B Matthews
- Departments of Psychology and Neuroscience, Baylor UniversityWaco, TX, USA
- Present address: Department of Psychology, Nanyang Technological UniversitySingapore
| | - G Mittleman
- Department of Psychology, The University of MemphisMemphis, TN
| | - D Goldowitz
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British ColumbiaVancouver, BC, Canada
| | - E J Chesler
- Systems Genetics Group, Biosciences Division, Oak Ridge National LaboratoryOak Ridge TN
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Gaglani SM, Lu L, Williams RW, Rosen GD. The genetic control of neocortex volume and covariation with neocortical gene expression in mice. BMC Neurosci 2009; 10:44. [PMID: 19426526 PMCID: PMC2685397 DOI: 10.1186/1471-2202-10-44] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Accepted: 05/09/2009] [Indexed: 11/10/2022] Open
Abstract
Background The size of the cerebral cortex varies widely within human populations, and a large portion of this variance is modulated by genetic factors. The discovery and characterization of these genes and their variants can contribute to an understanding of individual differences in brain development, behavior, and disease susceptibility. Here we use unbiased stereological techniques to map quantitative trait loci (QTLs) that modulate the volume of neocortex. Results We estimated volumes bilaterally in an expanded set of BXD recombinant inbred strains (n = 56 strains and 223 animals) taken from the Mouse Brain Library . We generated matched microarray data for the cerebral cortex in the same large panel of strains and in parental neonates to efficiently nominate and evaluate candidate genes. Volume of the neocortex varies widely, and is a heritable trait. Genome-wide mapping of this trait revealed two QTLs – one on chromosome (Chr) 6 at 88 ± 5 Mb and another at Chr 11 (41 ± 8 Mb). We generated both neonatal and adult neocortical gene expression databases using microarray technology. Using these databases in combination with other bioinformatic tools we have identified positional candidates on these QTL intervals. Conclusion This study is the first to use the expanded set of BXD strains to map neocortical volume, and we found that normal variation of this trait is, at least in part, genetically modulated. These results provide a baseline from which to assess the genetic contribution to regional variation in neocortical volume, as well as other neuroanatomic phenotypes that may contribute to variation in regional volume, such as proliferation, death, and number and packing density of neurons
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Affiliation(s)
- Shiv M Gaglani
- Department of Neurology, Division of Behavioral Neurology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
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15
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Rosen GD, Pung CJ, Owens CB, Caplow J, Kim H, Mozhui K, Lu L, Williams RW. Genetic modulation of striatal volume by loci on Chrs 6 and 17 in BXD recombinant inbred mice. GENES BRAIN AND BEHAVIOR 2009; 8:296-308. [PMID: 19191878 DOI: 10.1111/j.1601-183x.2009.00473.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Natural variation in the absolute and relative size of different parts of the human brain is substantial, with a range that often exceeds a factor of 2. Much of this variation is generated by the cumulative effects of sets of unknown gene variants that modulate the proliferation, growth and death of neurons and glial cells. Discovering and testing the functions of these genes should contribute significantly to our understanding of differences in brain development, behavior and disease susceptibility. We have exploited a large population of genetically well-characterized strains of mice (BXD recombinant inbred strains) to map gene variants that influence the volume of the dorsal striatum (caudate-putamen without nucleus accumbens). We used unbiased methods to estimate volumes bilaterally in a sex-balanced sample taken from the Mouse Brain Library (www.mbl.org). We generated a matched microarray data set to efficiently evaluate candidate genes (www.genenetwork.org). As in humans, volume of the striatum is highly heritable, with greater than twofold differences among strains. We mapped a locus that modulates striatal volume on chromosome (Chr) 6 at 88 +/- 5 Mb. We also uncovered an epistatic interaction between loci on Chr 6 and Chr 17 that modulates striatal volume. Using bioinformatic tools and the corresponding expression database, we have identified positional candidates in these quantitative trait locus intervals.
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Affiliation(s)
- G D Rosen
- Division of Behavioral Neurology, Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
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Kobeissy FH, Sadasivan S, Oli MW, Robinson G, Larner SF, Zhang Z, Hayes RL, Wang KKW. Neuroproteomics and systems biology-based discovery of protein biomarkers for traumatic brain injury and clinical validation. Proteomics Clin Appl 2008; 2:1467-83. [DOI: 10.1002/prca.200800011] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Indexed: 01/24/2023]
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17
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Bertrand L, Nissanov J. The Neuroterrain 3D Mouse Brain Atlas. Front Neuroinform 2008; 2:3. [PMID: 18974795 PMCID: PMC2525976 DOI: 10.3389/neuro.11.003.2008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 07/10/2008] [Indexed: 11/13/2022] Open
Abstract
A significant objective of neuroinformatics is the construction of tools to readily access, search, and analyze anatomical imagery. This goal can be subdivided into development of the necessary databases and of the computer vision tools for image analysis. When considering mesoscale images, the latter tools can be further divided into registration algorithms and anatomical models. The models are atlases that contain both bitmap images and templates of anatomical boundaries. We report here on construction of such a model for the C57BL/6J mouse. The intended purpose of this atlas is to aid in automated delineation of the Mouse Brain Library, a database of brain histological images of importance to neurogenetic research.
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Affiliation(s)
- Louise Bertrand
- Department of Neurobiology and Anatomy, Drexel University College of MedicinePhiladelphia, PA, USA
| | - Jonathan Nissanov
- Department of Neurobiology and Anatomy, Drexel University College of MedicinePhiladelphia, PA, USA
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Boline J, Lee EF, Toga AW. Digital atlases as a framework for data sharing. Front Neurosci 2008; 2:100-6. [PMID: 18982112 PMCID: PMC2570073 DOI: 10.3389/neuro.01.012.2008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 05/22/2008] [Indexed: 11/30/2022] Open
Abstract
Digital brain atlases are useful as references, analytical tools, and as a data integration framework. As a result, they and their supporting tools are being recognized as potentially useful resources in the movement toward data sharing. Several projects are connecting infrastructure to these tools which facilitate sharing, managing, and retrieving data of different types, scale, and even location. With these in place, we have the ability to combine, analyze, and interpret these data in a manner not previously possible, opening the door to examine issues in new and exciting ways, and potentially leading to speedier discovery of answers as well as new questions about the brain. Here we discuss recent efforts in the use of digital mouse atlases for data sharing.
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Affiliation(s)
- Jyl Boline
- Department of Neurology, Laboratory of NeuroImaging, School of Medicine, University of California Los Angeles Los Angeles, CA, USA
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19
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Abstract
Neuroinformatics seeks to create and maintain web-accessible databases of experimental and computational data, together with innovative software tools, essential for understanding the nervous system in its normal function and in neurological disorders. Neuroinformatics includes traditional bioinformatics of gene and protein sequences in the brain; atlases of brain anatomy and localization of genes and proteins; imaging of brain cells; brain imaging by positron emission tomography (PET), functional magnetic resonance imaging (fMRI), electroencephalography (EEG), magnetoencephalography (MEG) and other methods; many electrophysiological recording methods; and clinical neurological data, among others. Building neuroinformatics databases and tools presents difficult challenges because they span a wide range of spatial scales and types of data stored and analyzed. Traditional bioinformatics, by comparison, focuses primarily on genomic and proteomic data (which of course also presents difficult challenges). Much of bioinformatics analysis focus on sequences (DNA, RNA, and protein molecules), as the type of data that are stored, compared, and sometimes modeled. Bioinformatics is undergoing explosive growth with the addition, for example, of databases that catalog interactions between proteins, of databases that track the evolution of genes, and of systems biology databases which contain models of all aspects of organisms. This commentary briefly reviews neuroinformatics with clarification of its relationship to traditional and modern bioinformatics.
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Affiliation(s)
- Thomas M Morse
- Department of Neurobiology, Yale University School of Medicine, 336 Cedar Street, New Haven, CT 06510, USA.
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Bug W, Gustafson C, Shahar A, Gefen S, Fan Y, Bertrand L, Nissanov J. Brain spatial normalization. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2008; 401:211-34. [PMID: 18368369 DOI: 10.1007/978-1-59745-520-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Neuroanatomical informatics, a subspecialty of neuroinformatics, focuses on technological solutions to neuroimage database access. Its current main goal is an image-based query system that is able to retrieve imagery based on anatomical location. Here, we describe a set of tools that collectively form such a solution for sectional material and that are available to investigators to use on their own data sets. The system accepts slide images as input and yields a matrix of transformation parameters that map each point on the input image to a standardized 3D brain atlas. In essence, this spatial normalization makes the atlas a spatial indexer from which queries can be issued simply by specifying a location on the reference atlas. Our objective here is to familiarize potential users of the system with the steps required of them as well as steps that take place behind the scene. We detail the capabilities and the limitations of the current implementation and briefly describe the enhancements planned for the near future.
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Affiliation(s)
- William Bug
- Laboratory for Bioimaging and Anatomical Informatics, Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA
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Gefen S, Kiryati N, Nissanov J. Atlas-Based Indexing of Brain Sections via 2-D to 3-D Image Registration. IEEE Trans Biomed Eng 2008; 55:147-56. [DOI: 10.1109/tbme.2007.899361] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Nazor KE, Seward T, Telling GC. Motor behavioral and neuropathological deficits in mice deficient for normal prion protein expression. Biochim Biophys Acta Mol Basis Dis 2007; 1772:645-53. [PMID: 17531449 PMCID: PMC3025296 DOI: 10.1016/j.bbadis.2007.04.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 04/12/2007] [Accepted: 04/17/2007] [Indexed: 10/23/2022]
Abstract
It has been difficult to reconcile the absence of pathology and apparently normal behavior of mice lacking prion protein (PrP), referred to as Prnp(0/0) mice, with a mechanism of prion pathogenesis involving progressive loss of PrP(C)-mediated neuroprotection. However, here we report that Prnp(0/0) mice exhibit significant age-related defects in motor coordination and balance compared with mice expressing wild type Prnp on a syngeneic background, and that the brains of behaviorally-impaired Prnp(0/0) mice display the cardinal neuropathological hallmarks of spongiform pathology and reactive astrocytic gliosis that normally accompany prion disease. Consistent with the appearance of cerebellar ataxia as an early symptom in patients with Gerstmann-Sträussler-Scheinker syndrome (GSS), an inherited form of human prion disease, motor coordination and balance defects manifested in a transgenic (Tg) mouse model of GSS considerably earlier than the onset of end-stage neurodegenerative disease. Our results are consistent with a mechanism in which loss of normal PrP(C) function is an important pathological component of prion diseases.
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Affiliation(s)
- Karah E. Nazor
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY
- Graduate Center for Gerontology, University of Kentucky, Lexington, KY
| | - Tanya Seward
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Glenn C. Telling
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY
- Graduate Center for Gerontology, University of Kentucky, Lexington, KY
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY
- Department of Neurology, University of Kentucky, Lexington, KY
- To whom correspondence should be addressed: 332 Health Sciences Research Building, University of Kentucky, 800 Rose Street, Lexington, KY 40536. Tel: (859) 323-8564; Fax (859) 257-6151;
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Braude I, Marker J, Museth K, Nissanov J, Breen D. Contour-Based Surface Reconstruction using MPU Implicit Models. GRAPHICAL MODELS 2007; 69:139-157. [PMID: 18496609 PMCID: PMC2390921 DOI: 10.1016/j.gmod.2006.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This paper presents a technique for creating a smooth, closed surface from a set of 2D contours, which have been extracted from a 3D scan. The technique interprets the pixels that make up the contours as points in ℝ(3) and employs Multi-level Partition of Unity (MPU) implicit models to create a surface that approximately fits to the 3D points. Since MPU implicit models additionally require surface normal information at each point, an algorithm that estimates normals from the contour data is also described. Contour data frequently contains noise from the scanning and delineation process. MPU implicit models provide a superior approach to the problem of contour-based surface reconstruction, especially in the presence of noise, because they are based on adaptive implicit functions that locally approximate the points within a controllable error bound. We demonstrate the effectiveness of our technique with a number of example datasets, providing images and error statistics generated from our results.
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Affiliation(s)
- Ilya Braude
- Department of Computer Science, Drexel University, Philadelphia, PA
| | - Jeffrey Marker
- Department of Computer Science, Drexel University, Philadelphia, PA
| | - Ken Museth
- Department of Science and Technology, Linköping University, Norrköping, Sweden
| | - Jonathan Nissanov
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA
| | - David Breen
- Department of Computer Science, Drexel University, Philadelphia, PA
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Moene IA, Subramaniam S, Darin D, Leergaard TB, Bjaalie JG. Toward a workbench for rodent brain image data systems architecture and design. Neuroinformatics 2007; 5:35-58. [PMID: 17426352 DOI: 10.1385/ni:5:1:35] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/11/2022]
Abstract
We present a novel system for storing and manipulating microscopic images from sections through the brain and higher-level data extracted from such images. The system is designed and built on a three-tier paradigm and provides the research community with a web-based interface for facile use in neuroscience research. The Oracle relational database management system provides the ability to store a variety of objects relevant to the images and provides the framework for complex querying of data stored in the system. Further, the suite of applications intimately tied into the infrastructure in the application layer provide the user the ability not only to query and visualize the data, but also to perform analysis operations based on the tools embedded into the system. The presentation layer uses extant protocols of the modern web browser and this provides ease of use of the system. The present release, named Functional Anatomy of the Cerebro-Cerebellar System (FACCS), available through The Rodent Brain Workbench (http:// rbwb.org/), is targeted at the functional anatomy of the cerebro-cerebellar system in rats, and holds axonal tracing data from these projections. The system is extensible to other circuits and projections and to other categories of image data and provides a unique environment for analysis of rodent brain maps in the context of anatomical data. The FACCS application assumes standard animal brain atlas models and can be extended to future models. The system is available both for interactive use from a remote web-browser client as well as for download to a local server machine.
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Affiliation(s)
- Ivar A Moene
- Neural Systems and Graphics Computing Laboratory, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, PO Box 1105 Blindern, N-0317 Oslo, Norway
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NeuroTerrain--a client-server system for browsing 3D biomedical image data sets. BMC Bioinformatics 2007; 8:40. [PMID: 17280615 PMCID: PMC1802997 DOI: 10.1186/1471-2105-8-40] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Accepted: 02/05/2007] [Indexed: 11/18/2022] Open
Abstract
Background Three dimensional biomedical image sets are becoming ubiquitous, along with the canonical atlases providing the necessary spatial context for analysis. To make full use of these 3D image sets, one must be able to present views for 2D display, either surface renderings or 2D cross-sections through the data. Typical display software is limited to presentations along one of the three orthogonal anatomical axes (coronal, horizontal, or sagittal). However, data sets precisely oriented along the major axes are rare. To make fullest use of these datasets, one must reasonably match the atlas' orientation; this involves resampling the atlas in planes matched to the data set. Traditionally, this requires the atlas and browser reside on the user's desktop; unfortunately, in addition to being monolithic programs, these tools often require substantial local resources. In this article, we describe a network-capable, client-server framework to slice and visualize 3D atlases at off-axis angles, along with an open client architecture and development kit to support integration into complex data analysis environments. Results Here we describe the basic architecture of a client-server 3D visualization system, consisting of a thin Java client built on a development kit, and a computationally robust, high-performance server written in ANSI C++. The Java client components (NetOStat) support arbitrary-angle viewing and run on readily available desktop computers running Mac OS X, Windows XP, or Linux as a downloadable Java Application. Using the NeuroTerrain Software Development Kit (NT-SDK), sophisticated atlas browsing can be added to any Java-compatible application requiring as little as 50 lines of Java glue code, thus making it eminently re-useable and much more accessible to programmers building more complex, biomedical data analysis tools. The NT-SDK separates the interactive GUI components from the server control and monitoring, so as to support development of non-interactive applications. The server implementation takes full advantage of data center's high-performance hardware, where it can be co-localized with centrally-located, 3D dataset repositories, extending access to the researcher community throughout the Internet. Conclusion The combination of an optimized server and modular, platform-independent client provides an ideal environment for viewing complex 3D biomedical datasets, taking full advantage of high-performance servers to prepare images and subsets of associated meta-data for viewing, as well as the graphical capabilities in Java to actually display the data.
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26
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Rosen GD, Chesler EJ, Manly KF, Williams RW. An informatics approach to systems neurogenetics. Methods Mol Biol 2007; 401:287-303. [PMID: 18368372 DOI: 10.1007/978-1-59745-520-6_16] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We outline the theory behind complex trait analysis and systems genetics and describe web-accessible resources including GeneNetwork (GN) that can be used for rapid exploratory analysis and hypothesis testing. GN, in particular, is a tightly integrated suite of bioinformatics tools and data sets, which supports the investigation of complex networks of gene variants, molecules, and cellular processes that modulate complex traits, including behavior and disease susceptibility. Using various statistical tools, users are able to analyze gene expression in various brain regions and tissues, map loci that modulate these traits, and explore genetic covariance among traits. Taken together, these tools enable the user to begin to assess complex interactions of gene networks, and facilitate analysis of traits using a systems approach.
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Affiliation(s)
- Glenn D Rosen
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
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MacKenzie-Graham AJ, Lee EF, Dinov ID, Yuan H, Jacobs RE, Toga AW. Multimodal, multidimensional models of mouse brain. Epilepsia 2007; 48 Suppl 4:75-81. [PMID: 17767578 PMCID: PMC3192853 DOI: 10.1111/j.1528-1167.2007.01244.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Naturally occurring mutants and genetically manipulated strains of mice are widely used to model a variety of human diseases. Atlases are an invaluable aid in understanding the impact of such manipulations by providing a standard for comparison and to facilitate the integration of anatomic, genetic, and physiologic observations from multiple subjects and experiments. We have developed digital atlases of the C57BL/6J mouse brain (adult and neonate) as comprehensive frameworks for storing and accessing the myriad types of information about the mouse brain. Along with raw and annotated images, these contain database management systems and a set of tools for comparing information from different techniques and different animals. Each atlas establishes a canonical representation of the mouse brain and provides the tools for the manipulation and analysis of new data. We describe both these atlases and discuss how they may be put to use in organizing and analyzing data from mouse models of epilepsy.
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Affiliation(s)
| | - Erh-Fang Lee
- Laboratory of Neuro Imaging, University of California, Los Angeles, California, U.S.A
| | - Ivo D. Dinov
- Laboratory of Neuro Imaging, University of California, Los Angeles, California, U.S.A
| | - Heng Yuan
- Laboratory of Neuro Imaging, University of California, Los Angeles, California, U.S.A
| | - Russell E. Jacobs
- Beckman Institute, California Institute of Technology, Pasadena, California, U.S.A
| | - Arthur W. Toga
- Laboratory of Neuro Imaging, University of California, Los Angeles, California, U.S.A
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Mozhui K, Hamre KM, Holmes A, Lu L, Williams RW. Genetic and Structural Analysis of the Basolateral Amygdala Complex in BXD Recombinant Inbred Mice. Behav Genet 2006; 37:223-43. [PMID: 17131200 DOI: 10.1007/s10519-006-9122-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Accepted: 10/13/2006] [Indexed: 12/21/2022]
Abstract
The amygdala integrates and coordinates emotional and autonomic responses. The genetics that underlie variation in amygdala structure may be coupled to variation in levels of aggression, fear, anxiety, and affiliated behaviors. We systematically quantified the volume and cell populations of the basolateral amygdala complex (BLAc) across 35 BXD recombinant inbred (RI) lines, the parental strains--C57BL/6J (B6) and DBA/2J (D2)--and F1 hybrids (n cases=199, bilateral analysis). Neuron number and volume vary 1.7- to 2-fold among strains (e.g., neuron number ranged from 88,000 to 170,000). Glial and endothelial populations ranged more widely (5- to 8-fold), in part because of higher technical error. A quantitative trait locus (QTL) for the BLAc size is located on chromosome (Chr) 8 near the Large gene. This locus may also influence volume of other regions including hippocampus and cerebellum. Cell populations in the BLAc appear to be modulated more weakly by loci on Chrs 11 and 13. Candidate genes were selected on the basis of correlation with BLAc traits, chromosomal location, single nucleotide polymorphism (SNP) density, and expression patterns in the Allen Brain Atlas. Neurod2, a gene shown to be significant for the formation of the BLAc by knockout studies, is among the candidates genes. Other candidates include Large, and Thra. Responses to drugs of abuse and locomotor activity were the most notable behavioral correlates of the BLAc traits.
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Affiliation(s)
- Khyobeni Mozhui
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, 855 Monroe Avenue, Memphis, TN 38163, USA
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29
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Boy J, Leergaard TB, Schmidt T, Odeh F, Bichelmeier U, Nuber S, Holzmann C, Wree A, Prusiner SB, Bujard H, Riess O, Bjaalie JG. Expression mapping of tetracycline-responsive prion protein promoter: digital atlasing for generating cell-specific disease models. Neuroimage 2006; 33:449-62. [PMID: 16931059 DOI: 10.1016/j.neuroimage.2006.05.055] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 03/17/2006] [Accepted: 05/12/2006] [Indexed: 10/24/2022] Open
Abstract
We present a digital atlas system that allows mapping of molecular expression patterns at cellular resolution through large series of histological sections. Using this system, we have mapped the distribution of a distinct marker, encoded by the LacZ reporter gene driven by the tetracycline-responsive prion protein promoter in double transgenic mice. The purpose is to evaluate the suitability of this promoter mouse line for targeting genes of interest to specific brain regions, essential for construction of inducible transgenic disease models. Following processing to visualize the promoter expression, sections were counterstained to simultaneously display cytoarchitectonics. High-resolution mosaic images covering entire coronal sections were collected through the mouse brain at intervals of 200 microm. A web-based application provides access to a customized virtual microscopy tool for viewing and navigation within and across the section images. For each section image, the nearest section in a standard atlas is defined, and annotations of key structures and regions inserted. Putative categorization of labeled cells was performed with use of distribution patterns, followed by cell size and shape, as parameters that were compared to legacy data. Among the ensuing results were expression of this promoter in putative glial cells in the cerebellum (and not in Purkinje cells), in putative glial cells in the substantia nigra, in pallidal glial cells or interneurons, and in distinct cell layers and regions of the hippocampus. The study serves as a precursor for a database resource allowing evaluation of the suitability of different promoter mouse lines for generating disease models.
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Affiliation(s)
- Jana Boy
- Department of Medical Genetics, University of Tübingen, Tübingen, Germany
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Beatty J, Laughlin RE. Genomic regulation of natural variation in cortical and noncortical brain volume. BMC Neurosci 2006; 7:16. [PMID: 16503985 PMCID: PMC1402304 DOI: 10.1186/1471-2202-7-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Accepted: 02/17/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The relative growth of the neocortex parallels the emergence of complex cognitive functions across species. To determine the regions of the mammalian genome responsible for natural variations in cortical volume, we conducted a complex trait analysis using 34 strains of recombinant inbred (Rl) strains of mice (BXD), as well as their two parental strains (C57BL/6J and DBA/2J). We measured both neocortical volume and total brain volume in 155 coronally sectioned mouse brains that were Nissl stained and embedded in celloidin. After correction for shrinkage, the measured cortical and noncortical brain volumes were entered into a multiple regression analysis, which removed the effects of body size and age from the measurements. Marker regression and interval mapping were computed using WebQTL. RESULTS An ANOVA revealed that more than half of the variance of these regressed phenotypes is genetically determined. We then identified the regions of the genome regulating this heritability. We located genomic regions in which a linkage disequilibrium was present using WebQTL as both a mapping engine and genomic database. For neocortex, we found a genome-wide significant quantitative trait locus (QTL) on chromosome 11 (marker D11Mit19), as well as a suggestive QTL on chromosome 16 (marker D16Mit100). In contrast, for noncortex the effect of chromosome 11 was markedly reduced, and a significant QTL appeared on chromosome 19 (D19Mit22). CONCLUSION This classic pattern of double dissociation argues strongly for different genetic factors regulating relative cortical size, as opposed to brain volume more generally. It is likely, however, that the effects of proximal chromosome 11 extend beyond the neocortex strictly defined. An analysis of single nucleotide polymorphisms in these regions indicated that ciliary neurotrophic factor (Cntf) is quite possibly the gene underlying the noncortical QTL. Evidence for a candidate gene modulating neocortical volume was much weaker, but Otx1 deserves further consideration.
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Affiliation(s)
- Jackson Beatty
- Department of Psychology, University of California Los Angeles, Los Angeles, California, USA
| | - Rick E Laughlin
- Department of Psychology, University of California Los Angeles, Los Angeles, California, USA
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Li Y, Brewer D, Burke RE, Ascoli GA. Developmental changes in spinal motoneuron dendrites in neonatal mice. J Comp Neurol 2005; 483:304-17. [PMID: 15682391 DOI: 10.1002/cne.20438] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We examined the age-dependent morphological changes of lumbar spinal motoneurons (MNs) in neonatal Swiss-Webster mice during the first 2 weeks of postnatal life. Neurons labeled by intracellular injection of biocytin in hemisected lumbosacral spinal cords in vitro were reconstructed from serial sections. Digitized data were compared for young (P3; postnatal days 2-4; n = 9) and older animals (P11; postnatal days 10-13; n = 8). As expected, measures of dendritic size (e.g., stem branch diameter, total surface area, maximum distance to tips, and lateral tree spread) were all significantly greater for P11 than for P3 mice. In contrast, the number of dendrites per MN and parameters related to tree topology (e.g., terminations per tree and maximum branch order), although slightly greater for P11 animals, were not significantly different between the two ages. Dendrite growth appeared to be proportional throughout the tree because the ratios between average terminal and internal branch lengths were similar for the two groups. Furthermore, this elongation was proportional to enlargement of overall spinal cord dimensions. A variety of other morphometric measures showed no significant difference between age groups. The relative constancy of MN dendritic topology up to P13 was surprising, given the striking maturation in motor function during this time period.
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Affiliation(s)
- Yan Li
- Laboratory of Neural Control, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
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32
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Abstract
Hypothesis driven research has been shown to be an excellent model for pursuing investigations in neuroscience. The Human Genome Project demonstrated the added value of discovery research, especially in areas where large amounts of data are produced. Neuroscience has become a data rich field, and one that would be enhanced by incorporating the discovery approach. Databases, as well as analytical, modeling and simulation tools, will have to be developed, and they will need to be interoperable and federated. This paper presents an overview of the development of the field of neuroscience databases and associate tools: Neuroinformatics. The primary focus is on the impact of NIH funding of this process. The important issues of data sharing, as viewed from the perspective of the scientist and private and public funding organizations, are discussed. Neuroinformatics will provide more than just a sophisticated array of information technologies to help scientists understand and integrate nervous system data. It will make available powerful models of neural functions and facilitate discovery, hypothesis formulation and electronic collaboration.
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Airey DC, Robbins AI, Enzinger KM, Wu F, Collins CE. Variation in the cortical area map of C57BL/6J and DBA/2J inbred mice predicts strain identity. BMC Neurosci 2005; 6:18. [PMID: 15774010 PMCID: PMC1079866 DOI: 10.1186/1471-2202-6-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Accepted: 03/17/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent discoveries suggest that arealization of the mammalian cortical sheet develops in a manner consonant with principles established for embryonic patterning of the body. Signaling centers release morphogens that determine regional growth and tissue identity by regulating regional expression of transcription factors. Research on mouse cortex has identified several candidate morphogens that affect anteroposterior or mediolateral cortical regionalization as well as mitogenesis. Inbred strains of laboratory mice can be exploited to study cortical area map formation if there are significant phenotypic differences with which to correlate gene polymorphism or expression data. Here we describe differences in the cortical area map of two commonly used inbred strains of laboratory mice, C57BL/6J and DBA/2J. Complete cortical hemispheres from adult mice were dissected and stained for the cytochrome oxidase enzyme in order to measure histochemically defined cortical areas. RESULTS C57BL/6J has the larger neocortex, relatively larger primary visual cortex (V1), but relatively smaller posterior medial barrel subfield of the primary somatosensory cortex (PMBSF). The sample of C57BL/6J and DBA/2J mice can be discriminated with 90% accuracy on the basis of these three size dimensions. CONCLUSION C57BL/6J and DBA/2J have markedly different cortical area maps, suggesting that inbred strains harbor enough phenotypic variation to encourage a forward genetic approach to understanding cortical development, complementing other approaches.
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Affiliation(s)
- David C Airey
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alicia I Robbins
- Department of Psychology, Vanderbilt University, Nashville, TN, USA
| | | | - Fangbai Wu
- Department of Psychology, Vanderbilt University, Nashville, TN, USA
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Baldock RA, Bard JBL, Burger A, Burton N, Christiansen J, Feng G, Hill B, Houghton D, Kaufman M, Rao J, Sharpe J, Ross A, Stevenson P, Venkataraman S, Waterhouse A, Yang Y, Davidson DR. EMAP and EMAGE: a framework for understanding spatially organized data. Neuroinformatics 2004; 1:309-25. [PMID: 15043218 DOI: 10.1385/ni:1:4:309] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Edinburgh MouseAtlas Project (EMAP) is a time-series of mouse-embryo volumetric models. The models provide a context-free spatial framework onto which structural interpretations and experimental data can be mapped. This enables collation, comparison, and query of complex spatial patterns with respect to each other and with respect to known or hypothesized structure. The atlas also includes a time-dependent anatomical ontology and mapping between the ontology and the spatial models in the form of delineated anatomical regions or tissues. The models provide a natural, graphical context for browsing and visualizing complex data. The Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) is one of the first applications of the EMAP framework and provides a spatially mapped gene-expression database with associated tools for data mapping, submission, and query. In this article, we describe the underlying principles of the Atlas and the gene-expression database, and provide a practical introduction to the use of the EMAP and EMAGE tools, including use of new techniques for whole body gene-expression data capture and mapping.
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Affiliation(s)
- Richard A Baldock
- MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, UK.
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Abstract
WebQTL is a website that combines databases of complex traits with fast software for mapping quantitative trait loci (QTLs) and for searching for correlations among traits. WebQTL also includes well-curated genotype data for five sets of mouse recombinant inbred (RI) lines. Thus, to identify QTLs, users need provide only quantitative trait data from one of the supported populations. The WebQTL databases include both biological traits--neuroanatomical, pharmacological, and behavioral traits--and microarray-based gene expression data from BXD RI lines. A search function finds correlations between RNA expression and biological traits, and mapping functions find QTLs for either type of trait. The WebQTL service is available at http://www.webqtl.org/.
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Affiliation(s)
- Jintao Wang
- Department of Molecular & Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
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Martone ME, Zhang S, Gupta A, Qian X, He H, Price DL, Wong M, Santini S, Ellisman MH. The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. Neuroinformatics 2004; 1:379-95. [PMID: 15043222 DOI: 10.1385/ni:1:4:379] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The creation of structured shared data repositories for molecular data in the form of web-accessible databases like GenBank has been a driving force behind the genomic revolution. These resources serve not only to organize and manage molecular data being created by researchers around the globe, but also provide the starting point for data mining operations to uncover interesting information present in the large amount of sequence and structural data. To realize the full impact of the genomic and proteomic efforts of the last decade, similar resources are needed for structural and biochemical complexity in biological systems beyond the molecular level, where proteins and macromolecular complexes are situated within their cellular and tissue environments. In this review, we discuss our efforts in the development of neuroinformatics resources for managing and mining cell level imaging data derived from light and electron microscopy. We describe the main features of our web-accessible database, the Cell Centered Database (CCDB; http://ncmir.ucsd.edu/CCDB/), designed for structural and protein localization information at scales ranging from large expanses of tissue to cellular microdomains with their associated macromolecular constituents. The CCDB was created to make 3D microscopic imaging data available to the scientific community and to serve as a resource for investigating structural and macromolecular complexity of cells and tissues, particularly in the rodent nervous system.
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Affiliation(s)
- Maryann E Martone
- Department of Neurosciences, University of California at San Diego, San Diego, CA, USA.
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