RP+Research

Research Questions: Whats animals show similar genotypes? Is gene expression highly conserved? What is the structure of the rhodopsin protein? How does the chromophore work on a molecular basis?

**Gene focus: For my genetic research I chose to use __RHO__ or the rhodopsin gene as my gene of interest. My choice was based on the fact that is much more information known about this gene compared to USH2A and RPGR.** Methods: ** BLASTn- This tool was used to find out what other organisms had a similar rhodopsin sequences.After using BLAST the organisms chosen were: ** 1. macaca fascicularis- long-tailed macaque 2. zalophus californianus- california sea lion 3. odobenus rosmarus- walrus 4. lephonychotes weddellii- weddell sea lion 5. ursus maritimus- polar bear 6. phoca hispida- ringed seal 7. erignathus barbatus- bearded seal 8. mirounga angustirostris- northern elephant seal 9. enhydra lutris- sea otter 10. phoca groenlandica- harp seal

MEGA- This tool was used give a numerical and visual relationship between the different organisms. In the program MEGA the 11 sequences were aligned using these parameters under __multiple alignment__ using **Clusta**l: Gap Opening Penalty: 15 Gap Extension Penalty: 6.66 DNA weight matrix: IUB Transition Weight: .5

-A maximum likely phylogenetic tree was then made and bootstrap values were calculated:

__Analysis__: All of the calculated bootstrap values are above 70, which means the sequences are similar enough to validity to this phylogeny. The only to note would be that the macaque and the human are on their own separate branch, which makes sense due to the fact that primates are known more closely related to humans. The sequences for the macaque and the human were also notably longer because the other organisms only had partial sequences when searched. The partial sequences do seem to have similarities with humans though. It is also interesting that all of the organisms that came as similar when searched in BLAST happened to be sea dwelling mammals. This could support the theory that humans evolved from the sea long ago.

Protein Data Bank- Used to find the structure of rhodopsin and it's description

__Analysis of Structure__: Rhodopsin is a transmembrane protein that is responsible for light detection. The protein consists of 7 connected alpha helices. Nestled within the helices is the molecule 11-cis-retinol, which is the key component in light detection. In this diagram 11-cis-retinol is the small grey molecule in the thick bunch of pink helices. When light hits the molecule it changes to its trans isomer, but it can't change back automatically, so it is removed from rhodopsin to a nearby cell and isomermase converts back to it's original form.

PubChem by NCBI- It was used to find the structure of the molecule that gives rhodopsin its functionality


 * __Analysis of Molecular Structure__**: The molecule above is known as the chromophore 11-cis-retinol, which is a molecule that gives off a color when wavelengths of light hit it. In rhodopsin this molecule sits in the center and starts the chain reaction that allows the brain to sense light. When photons hit this molecule it changes it position to trans. Cis means that both carbons are on the same side of the double bond. Trans is when they are on different sides. In most cases trans is the more stable form, which is most likely why this molecule reacts when light hits it.


 * Conclusions**: After using the human gene RHO in BLAST, the results tended to show that water dwelling mammals had the most closely related sequence and the sequence seemed to be highly conserved throughout the group. From the structure of the protein and the molecule within the protein, the mechanism of vision can somewhat be understood. The factor that initiates our ability to see light and dark lies within the center of the rhodopsin. These conclusions can be used to dive deeper into the subject because these orgasms can be used to model the human rhodopsin gene and problems with the rhodopsin and chromophore can be linked to mutations.


 * What's Next**: Like it was stated above, the mutations should be linked with the chromophore and rhodopsin, and these animals could be possible candidates for a model. Although the chromophore and rhodopsin is only on of many factors that cause RP, it is definitely a step in the right direction.

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