Transcribe DNA sequences into music

In his book Gödel, Escher, Bach, Douglas Hofstadter makes an explicit analogy between genes and music:

Imagine the mRNA to be like a long piece of magnetic recording tape, and the ribosome to be like a tape recorder. As the tape passes through the playing head of the recorder, it is “read” and converted into music, or other sounds…When a “tape” of mRNA passes through the “playing head” of a ribosome, the “notes” produced are amino acids and the pieces of music they make up are proteins.

Music is not a mere linear sequence of notes. Our minds perceive pieces of music on a level far higher than that. We chunk notes into phrases, phrases into melodies, melodies into movements, and movements into full pieces. similarly proteins only make sense when they act as chunked units. Although a primary structure carries all the information for the tertiary structure to be created, it still “feels” like less, for its potential is only realized when the tertiary structure is actually physically created.

Now, using a program called Gene2Music, you can transcribe any DNA sequence into music. The program, which was developed by molecular geneticists Rie Takahashi and Jeffrey Miller of the University of California, Los Angeles, uses an algorithm that converts each codon in the DNA sequence into a musical chord. Codons for hydrophilic amino acids (which are attracted to water) have a high key, codons for hydrophobic amino acids (which are repelled by water) have a lower key, and the duration of each chord is determined by the frequency of its corresponding codon within the transcribed DNA sequence.

Using Gene2Music, Takahashi and Miller have so far generated more than a dozen pieces of music, including transcripts of the huntingtin and cytochrome c genes. The aim of the project is to make the visualization of proteins easier for scientists, and to make molecular biology more comprehensible to non-scientists. Takahashi says it was inspired by a blind meteorology student and Cornell University, who devised a method by which the different colours on a weather map could be converted into musical tones.

This isn’t the first time DNA sequences have been translated into music. In 1995, for example, the British band The Shamen collaborated with Ross King to produce a track called S2 Translation, which is based on the coding sequence for the 5HT-S2 receptor. The track was generated in a way that sounds similar to Takahashi’s and Miller’s method:

The number and nature of bass notes per codon/bar were determined by the hydrophobicity/hydrophilicity, ionic charge (positive or negative) and size of each amino acid residue (Proline, for example,which has no characteristics other than its small size, can be identified easily as the bars where the bass line ‘drops out’). The musical output resulting from these rules was further processed by mapping the notes onto different tonalities, both to make the piece more interesting, and to suggest the organisation of the protein molecule into regions of different secondary structure (although since S2 is a membrane protein and thus impossible to crystallise outside the lipid bilayer, this was definitely creative licence).

Previous pieces of DNA music have tended to sound unmelodic, because they often contain jump distances of up to two octaves (16 notes) from one tone to another. Takahashi and Miller overcame this by assigning three notes to each codon. With a triad chord for each codon, the differences between successive chords in the music are reduced.

Reversal of memory impairments associated with Alzheimer’s

Photo Sharing and Video Hosting at PhotobucketResearchers from the Picower Institute for Learning and Memory at MIT, with collaborators from the Howard Hughes Medical Institute, report that an enriched environment can restore memory in mice with Alzheimer’s-like neurodegeneration. Further, they determined the effects of the enriched environment on gene expression, and showed that the animals’ memory loss could also be reversed using a drug which mimicked those effects. The findings raise the possibility that drugs to treat the memory loss associated with Alzheimer’s Disease and other forms of dementia could be developed. They also suggest that mental stimulation could help reverse the amnesia in Alzheimer’s patients in the advanced stages of the disease.

Professor Li-Huei Tsai and her colleagues developed a transgenic mouse model of Alzheimer’s Disease, in which expression of a gene called p25 gene, which has been implicated in various neurodegenerative diseases, induces extensive neuronal cell death in spatially restricted regions of the forebrain. p25 expression can be induced at any point during the life of the transgenic animals by supplementing their diet with a chemical called doxycyclin.

Mice expressing the p25 transgene were trained to perform two memory tasks. One task tested the animals’ associative memory, the other tested their spatial memory. For the associative memory task, the mice were classically conditioned to fear a compartment in the enclosure in which they were kept. After repeatedly receiving mild electric shocks when placed in the compartment, the mice learnt to associate the two; afterwards, when returned to the compartment, they would freeze instead of exploring their environment, indicating that they were fearful of receiving a shock. The mice were also trained to perform a spatial memory task in which they find a platform submerged in murky water. When the animals reached 11 months of age, expression of the p25 gene was induced for a period of up to 6 weeks; as a result, the animals’ performance on both memory tasks was severely impaired.

The mice were then returned to their cages. The researchers added toys, running wheels and various other stimuli to the cages of one group of mice. The toys were changed on a daily basis for four weeks. Nothing was added to the cages in which the control mice were kept (the “home” cages). The performance of both groups of mice in the two memory tasks were then re-tested. It was found that the mice exposed to the enriched environment performed significantly better on both memory tasks than the control animals. When placed in the compartment that they had previously associated with an electric shock, the mice that had been kept in an enriched environment quickly froze, indicating that they once again remembered the association, and, when tested on the spatial memory task, they successfully located the submerged platform. In contrast, the control animals did not freeze when placed in the compartment in which they had received the electric shocks, and could not locate the submerged platform.

The researchers then examined the brains of the mice. First, the brains of both groups of animals were weighed, and it was found that there was no significant difference between the weight of the brains of both groups. Thus, the observed memory recovery occurred despite extensive neuronal death and loss of synapses. This suggests that rather than being “lost” altogether, the memories persist, so that it is retrieval, and not the encoded memories themselves, that are impaired by neurodegeneration. Antibody staining was used to compare the distribution of a number of synaptic in the two groups of animals. This showed that, in the brains of mice kept in an enriched environment, levels of the proteins MAP-2 and synaptophysin (which are both involved in synapse formation) were markedly increased in the hippocampus, which is known to be involved in the encoding of memories, and anterior cingulate cortex, which has been implicated in the consolidation of long-term memories. The data suggest that the enriched environment led to memory recovery by re-establishing the synaptic networks, and not by inducing growth of new nerve cells or nerve cell processes. (Comparison of MAP-2 expression in the CA1 region of the hippocampus in experimental and control animals is shown in the image at the top, from the Supplemental information accompanying the paper.)

Proteins called histones were then compared in the brains of the two groups of mice. Histones are closely associated with DNA – they act as spools around which DNA is tighly wrapped. A chromosome consists in equal parts of a single DNA molecule and histone proteins, which together are termed chromatin. Histones play a vital role in regulating gene expression; chemical modification of histones – by, for example, the addition or removal of acetyl (-COCH3) or methyl (-CH3) functional groups – causes the chromatin structure to open or close, so that the information contained within the DNA is made more or less accessible to the enzymes involved in protein synthesis. When Tsai’s group used antibody staining to examine the chromatin in their animals, they found that there was increased histone acetylation (addition of acetyl groups) in the hippocampi and cortices of mice that had been exposed to the enriched environment compared to the control animals. This was observed as little as 3 hours after exposure to the enriched environment. The enriched environment appeared to restore memory in the animals by remodelling the chromatin structure, thus enabling expression of the genes involved in the synaptic plasticity underlying memory.

Having established that the enriched environment leads to opening of the chromatin structure by acetylation, the researchers then sought to determine whether or not a drug that prevents removal of acetyl groups from histones could also restore memory. Another group of groups of animals was trained to perform the memory tasks before p25-mediated neurodegeneration was induced. One group of animals was then injected with sodium butyrate, a histone deacetylase inhibitor. The compound led to a significant improvement in the performance of the mice on the memory tasks, as evidenced by reduced freezing behaviour in the associative memory task and successful location of the submerged platform in the spatial memory task. Examination of the animals’ brains showed that the compound had exactly the same effect as exposure to an enriched environment – increased levels of the synaptic proteins MAP-25 and synaptophysin in the hippocampus and anterior cingulate cortex.

It has long been known that gene transcription is necessary for memory formation, but it is only very recently that epigenetics – changes in gene expression not linked to changes in the DNA sequence itself – has been implicated in memory. The findings of Tsai’s group therefore confirm the role of epigenetics in memory formation. They also implicate histone deacetylase enzymes as a potential new target for drugs to treat Alzheimer’s Disease and other neurodegenerative diseases in which memory is impaired; there is, however, no indication as yet that histone deacetylase inhibitors would have a beneficial effect in humans. And, while most researchers trying to develop treatments for such conditions have focused on the early stages of the disease process, with the aim of slowing or halting all together disease progression, these findings suggest that mental stimulation could slow, or perhaps reverse, the memory impairment that occurs at later stages.

Reference:

Fischer, A., et al. (2007). Recovery of learning and memory is associated with chromatin remodelling. Nature doi: 10.1038/nature05772. [Abstract]

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