March 6th 2008

Molly Schumer and Amanda Trail

Two Reviews
Preuss, T.M. Caceres, M., Oldham, M.C., Geschwind, D.H., (2003) Human Brain Evolution: Insights from microarrays. Nature Reviews Genetics 5:850.
Khatovich, P., Enard,W., Lachmann, M., Paabo, S. (2006) Evolution of primate gene expression. Nature Reviews Genetics 7:693.

And One Research Paper
Caceres, M., Lachuer, H., Zapala, M.A., Redmond, J.C., Kudo, L., Geschwind, D.H., Lockhart, D.J., Preuss, T.M., Barlow, C. (2003) Elevated gene expression levels distinglus human from non-human primate brains. PNAS 100(22):13030-13035.

Food by Laila and Margaret

Who is Who by Kelsey and Alex

Short Oligonucleotide arrays are a type of microarray that allows for the detection of RNAs at a very low concentration (one company that makes them Affymetrix, claims that you can unambiguously detect RNAs present in a 1/300,000 frequency). The arrays have upto 500,000 unique probes that correspond to >10,000 genes. To form the unique probes, multiple small sequences of around 25 base pairs are selected for each gene. Having redundant sequences on an array is important for detecting false positives, but unlike cDNA microarrays, oligonucleotide arrays contain unique sequences designed to hybridize to the same RNA.
General design information
An animation is available
A variation of this technique can be used to detect genotypic changes

cDNA microarrays operate on a similar hybridization principle but contain longer DNA sequences amplified by PCR from cDNA library clones and are then spotted onto treated glass slides. These arrays are most applicable to species for which full genome sequence is not available.
the NCBI site is very informative.
but also for an entertaining animation see the Davidson College website.


Glial cells are non-neuronal cells that are integral in neural function. They form the myelin sheath, maintain homeostasis, and provide protection and support for neurons.

Astrocytes are a type of glial cell that are now thought to signal to neurons and affect their activity. click

Fibroblasts make and maintain the extracellular matrix in some tissues, basically act as a tissue support structure.

Neutral theory is a theory of molecular evolution that states that the vast majority of mutations have a neutral effect on the fitness of the organism. This model predicts that new alleles arise though single-nucleotide mutations that accumulate linearly with time.  See “Evolution of Primate Gene Expression” article (pg 694) for more details.

Cluster analysis, or data segmentation, is the partitioning of (in this case) gene expression sequences into discrete species-specific groups.

Probe sets are a series of probes on an oligonucleotide array that collectively correspond to a specific cDNA. This set up allows for the recognition of species at different taxonomic levels and an assessment of biodiversity through microarray analysis.

Human specific pattern of hybridization refers to the sets of genes that were either up-regulated or down-regulated in the human arrays compared to the chimpanzees and rhesus macaques in this study.

Cis regulatory changes are regions of sequence adjacent to the gene of interest that affect regulation and expression of that gene. An example would be a mutation in a promoter region that causes increased expression, but cis regulatory elements can be up to 1 Mb away according to some papers.

Trans regulatory changes are elements that affect the regulation of a gene usually as an associated protein. As a result their corresponding sequence can be located anywhere in the genome and can have diverse and widespread effects on expression.