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Added by Chinh Dang, last edited by Chinh Dang on Jul 14, 2006  (view change)
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Latest Blog Postings 

Alan Boyle ran an informative blog about some of the Allen Institute's recent projects, and their impact on the scientific community.  Responses to the blog raise interesting questions about the impact of environmental toxins on neural function, and also highlight public interest regarding how basic research can establish a groundwork for studying challenging disease and injury models such as autism and spinal cord damage. 

Posted at 14 Mar @ 11:57 AM by Amy Bernard | 0 comments
Last changed Nov 28, 2007 17:35 by Carol Thompson

As of the November 15 release of the new website for the sleep deprivation in situ hybridization data, there are now 224 genes available for viewing. Additionally, a new method of visualizing expression differences between conditions is available: the "difference grid". The difference grid allows one to view differences in gene expression across 2 different experimental conditions (e.g., Sleep deprivation vs. time of day control) in a 3D Brain Explorer file for experiments with 3 replicates per condition.  Please check it out on the updated sleep website: sleep.alleninstitute.org

Please feel free to post questions about the use of these difference grids or other sleep website features.

Posted at 28 Nov @ 5:34 PM by Carol Thompson | 0 comments

Sleep deprivation impact memory, mood, and other cognitive processes. The Allen Institute is examining gene expression in the mouse brain in response to sleep deprivation to understand which particular regions or cell types are affected, and which genes are up- or down-regulated. The initial data for 48 genes is now available on the web - go to the gene search page, and click on "Sleep Study" under the Allen Institute Projects on the right side of the page. Use "Export all genes in Database" on the right hand side to find out what genes are available.

Posted at 09 Jan @ 10:15 AM by Carol Thompson | 2 comments

One of the fundamental questions driving research at the Allen Institute is how cortical circuitry underlies complex brain function. Understanding the cellular and molecular structure of these circuits is the first step but it is also important to understand how disturbances in these circuits influence function. One way to approach this is to examine differences that exist normal mice and those with impaired cortical functioning. Two human diseases that are associated with profound disruption of cognitive and emotional function are schizophrenia and autism. Schizophrenia is a chronic, disabling, neurological disorder. It is associated with disturbances in sensory perception (including hallucinations and delusion), impaired working or procedural memory, disorganized thoughts, and flattened affect. Autism is a developmental disorder that causes severe and pervasive impairment in cognitive flexibility, interpretation of feelings, language, the ability to relate to others, and atypical perception of somatosensory, visual, auditory, gustatory, and olfactory signals. Both of these disorders have been linked to defects in cortical development. Better classification of the changes in cortical connectivity that are associated with these diseases will lead to increased understanding of the correlation between structure and function. Since tissue from human patients is hard to obtain we will begin to address this question using animal models of schizophrenia and autism.
In order to assess structural defects in these mouse models we have identified molecular markers that specifically delineate subregions of the cortex, hippocampus and amygdala. These markers provide powerful tools for analysis of the fine cellular architecture of these structures, as well as a means to assess disorganization of normal brain architecture. 

An example of the power of molecular phenotyping to identify and characterize disorganized cellular architecture is shown in Figure 1, a panel of cortical layer-specific genes was used to characterize the laminar architecture of the neocortex in Reelin knockout mice.  Mice homozygous for the reeler (Relnrl) mutation exhibit an ataxic gait, dystonic posture and tremors starting around 2 weeks of age. This mouse has been extensively described as having inverted cortical layers due to a migration defect during migration of newly generated cortical neurons from the ventricular zone into the developing cortex.  The marker panel clearly shows cellular disorganization, but further demonstrates a more fundamental disorganization than simple inversion.  Application of these marker panels should reveal more subtle cellular abnormalities in mouse models of autistic spectrum disorders that are difficult to identify using conventional techniques.

Posted at 11 Sep @ 3:06 PM by MaureenH | 2 comments

A recent announcement in Science describes the kickoff of NIH's Knockout Mouse Project.  This project is one part of a multiple aims to create a knockout mouse for every gene in the mouse genome.  Along the same theme as the Allen Brain Atlas, the goal is to get complete coverage of the mouse genome, and allow researchers to use the resources that are generated by centers coordinated in this effort.  It's exciting to have the ability to view gene expression patterns on a genome-wide scale now with the Allen Brain Atlas, and know that soon the knockout resources will also be available to reserchers for all these genes.

Posted at 08 Sep @ 9:30 AM by Amy Bernard | 0 comments
Last changed Oct 02, 2006 14:26 by Anonymous
Labels: marco

This paper was published in Science and the authors find that

LMO41200

is more highly expressed on the right than in the left hemisphere.  The ABA has data for this gene in both the sagittal and the coronal planes.

Posted at 17 Jul @ 1:05 PM by Chinh Dang | 1 comment

Allen Institute Rolls Out 3D Brain Atlas Viewer;
Will Release Complete Data on 21K Genes in Fall
3D Brain Explorer enables users to view gene expression data in the mouse brain in three dimensions at 100-micron resolution.

http://www.bioinform.com for full article.

Posted at 17 Jul @ 8:50 AM by Chinh Dang | 0 comments
Last changed Jul 14, 2006 14:45 by Chinh Dang

John H. came to me last week inquiring about the ability to print an image from the Single Image Viewer without the Navigation Control.  At the time, I didn't think about it but there's actually an easy way to do this.

Launch the Single Image Viewer.  Click on "More Tools" and  select Image Viewer Setup.  Look at the below screen shot for example.


 

Posted at 14 Jul @ 2:45 PM by Chinh Dang | 0 comments

CYP1A2has been studied in humans for its role in coffee metabolism. A Nature article explains:
"In the new study, researchers specifically tested whether caffeine in coffee could promote heart problems by examining a gene called CYP1A2. The gene, which codes for an enzyme that helps to break down caffeine, comes in two flavours: one version, known as CYP1A2*1F, metabolizes caffeine more slowly than the other."

Posted at 14 Jul @ 2:36 PM by Chinh Dang | 0 comments
Last changed Jul 14, 2006 14:29 by Chinh Dang

The NYTimes.com mentions the gene syntrophin, gamma 1 (Sntg1) in a story about continuing selection pressures on human genes.

Posted at 14 Jul @ 2:29 PM by Chinh Dang | 0 comments
Last changed Jul 14, 2006 14:24 by Chinh Dang

This Genome News Network articlediscusses the similarity between a mouse's chromosome 16 and that of a human. In the Allen Brain Atlas, you can search for genes that appear on chromosome 16 in mice by using the query chromosome=16.

Posted at 14 Jul @ 12:46 PM by Chinh Dang | 0 comments

 

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Hello ABA users or To whom it may concern,

      Are the images on the ABA posted such that the left side of the brain/image is on the left side of the screen or vice versal? I couldn't find any info in the methods section. Thanks for your help.

Posted by Anonymous at May 01, 2007 09:46

The short answer is that it's not guaranteed consistent;  in general, the right side of the brain should be on the left side of the image on a coronal section.  The left hemisphere is the hemisphere sectioned for almost all sagittal sections.  For coronal sections, it is possible that an image could be flipped, but most sections should be oriented such that right is left and left is right.

Posted by Anonymous at May 03, 2007 14:33

For sagittal data, all images represent the left hemisphere of the brain, ordered from left (outer) to right (midbrain). For coronal data, sections are presented with the left hemisphere on the left and right hemisphere on the right.

Two conflicting answers to the question posed by Anonymous regarding the correspondence of the coronal images on the ABA site with the actual left/right side of the brain. It is my feeling that we should side with the response posted by Ms. Dang rather than that posted by Anonymous.

Posted by Anonymous at May 08, 2007 07:08

As presented in the graphs, normalized (0, 100) relative to themselves, a standard? Are expression levels, densities of one gene comparable to another gene?

Posted by Anonymous at Jul 30, 2007 12:32
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