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https://github.com/androidbeingx/omic_research

Python class project in collab with @heloint and @anivalle. Using Entrez, Seq.io, regex, pandas
https://github.com/androidbeingx/omic_research

entrez investigation ncbi-database pandas protein python regex

Last synced: 11 days ago
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Python class project in collab with @heloint and @anivalle. Using Entrez, Seq.io, regex, pandas

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README 

        
Hypothesis

==============



### Chosen organisms:

- Organism A: Fruit Flies

- Organism B: Homo Sapiens



### Species of Organism A:

- Drosophila melanogaster

- Drosophila simulans

- Drosophila sechellia

- Drosophila yakuba

- Drosophila erecta

- Drosophila ananassae

- Drosophila suzukii

- Drosophila teissieri



### Chosen genes:

- Adh (Alcohol dehydrogenase)

- ADH1B (Alcohol dehydrogenase, prefered name: "All-trans-retinol dehydrogenase")



#### Motives

Comparing the Alcohol dehydrogenase (Adh) gene of the Drosophila family with

the Homo sapien's ADH1B gene, which is associated with alcohol intolerance,

seems an interesting combination and further investigation of it can provide a

unique opportunity to gain insights into the evolutionary history of

alcohol metabolism and the genetic basis of alcohol-related traits in diverse

organisms.



#### Hypothesis

In humans, mutations in the *Alcohol dehydrogenase* (ADH1B) gene have been

associated with a number of health problems, including alcohol intolerance,

flushing (redness and warmth of the skin after drinking alcohol) and an

increased risk of alcoholism. However, these conditions are relatively rare and

are usually caused by specific genetic variants of the Adh gene.



The Adh gene is present in fruit flies and other organisms. We are interested

in finding out how this gene varies in fruit flies, what variations and

similarities there are, in order to carry out an experimental study and thus be

able to treat diseases caused by mutations in this gene.



The human ADH1B gene is an orthologue of the Drosophila melanogaster alcohol

dehydrogenase (Adh) gene.

They derive from a common ancestral gene and have evolved to perform similar

functions in those species. In this case, the human ADH1B gene and the

Drosophila melanogaster Adh gene encode enzymes involved in alcohol metabolism.



It should be noted that although the function of the human ADH1B and Drosophila

melanogaster Adh genes is similar, the specific mutations and regulatory

regions of these genes may differ between the two species, resulting in

differences in the expression and activity of these genes. This is exactly what

we would like to exploit with our project.



#### About Alcohol dehydrogenase (Adh) gene

The Adh gene in different species of fruit flies will have variations in its

genetic sequence, but the overall function of the gene will remain the same,

i.e. the gene will be responsible for breaking down alcohol and will therefore

have a conserved domain.



Mutations in the alcohol dehydrogenase (Adh) gene can lead to changes in the

activity and stability of the alcohol dehydrogenase enzyme. This can lead to

alcohol intolerance and an increased risk of alcoholism in some individuals.



Specific variants in the alcohol dehydrogenase (Adh) gene have been

associated with alcohol intolerance in humans, such as ADH1B

alcohol dehydrogenase (prefered name is "all-trans-retinol dehydrogenase").



This variant result in reduced activity of the Adh enzyme, leading to a

build-up of acetaldehyde, a toxic intermediate product of alcohol metabolism,

in the body. This build-up causes the symptoms of alcohol intolerance, such as

flushing (redness and warmth of the skin after drinking alcohol), tachycardia,

nausea and headache.



(NOTE: It is important to note that not all people carrying these variants will

develop alcohol intolerance. Other factors such as general health, diet and the

presence of other genes that affect alcohol metabolism may also play a role.)



#### Conclusion

The results of the alignment of the Alcohol dehydrogenase gene from different

Drosophila species against the ADH1B gene from Homo sapiens show that the

identity percentage ranges from 34.55% to 38.75%, with the highest identity

found in Drosophila simulans and the lowest in Drosophila ananassae.



These results indicate that although they have the same function, alcohol metabolism, 

their structure is not comparable, resulting in these low scores.

In addition, to be sure, we performed a phylogenetic tree to measure the degree of 

differences between species.

The result was that the human gene is far removed from Drosophila. This reaffirms the 

results of the alignment study.



This indicates that the Alcohol dehydrogenase gene has evolved differently in each

of these species. Although the gene product is the only mostly preserved across the

Drosophila species studied.



However, more research is needed to determine whether the differences in the Alcohol

dehydrogenase gene affect alcohol metabolism in Drosophila and if these

differences could be used to develop treatments for alcohol intolerance

sickness.



Overall, the results of this study provide important insights into

the evolution and function of Alcohol dehydrogenase gene in different

Drosophila species, and may have implications for understanding the genetic

basis of alcohol metabolism in humans.



### References:



- [Drosophila melanogaster ADH gene](https://www.ncbi.nlm.nih.gov/gene/3771877/)



- [Drosophila melanogaster ADH gene orthologs](https://www.orthodb.org/?ncbi=6732347)

(Note: the human ADH1B2 is not listed here, because it is a variant of it, which is orthologous too.)



- [Orthologous gene in human is ADH1B](https://www.ncbi.nlm.nih.gov/gene/125/)



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