Phylogenetics

 

 

The DNA sequence that has been emailed to you is a mutant cDNA sequence derived from an organism that displays an altered phenotype to wild type organisms.
Using appropriate bioinformatic software and databases determine the following.

(1) What species is the wild type sequence derived from (give Linnaean and common species names)?
(2) What protein does the wild type sequence code for?
(3) Align the mutant and wild type cDNAs and answer the following questions.
a. How do the mutant and wild type DNA sequences differ?
b. What is the nucleotide position of the change in the mutant?
(4) Use appropriate software to deduce the protein sequence that the mutant cDNA encodes and align it with the wild type. Answer the following questions.
a. What is the codon position of the change in the mutant sequence?
b. What amino acid substitution results from the mutation?
(5) Briefly comment on the effect you think the mutation might have on the protein function using the results obtained in part 4.
(6) Use appropriate bioinformatic resources to find the most closely related human protein homolog of the wild type sequence.
(i) What is the percentage similarity between the wild type protein and the human protein?
(ii) Use appropriate literature to find out the subchromosomal location of the human gene encoding this protein and how many exons it has.
(7) Select 15 orthologs of NADH dehydrogenase subunit 3 protein sequence from an evolutionary diverse cross section of bilateria species including human and align these using Clustal. Show the Clustal alignment output obtained. Use appropriate journal literature to find features and amino acids and highlight these in the alignment. Comment on the evolutionary conservation of these in less than 150 words.
(8) Using the data obtained in question 7 select an appropriate protein sequence as an outgroup and draw a phylogenetic tree. Comment on whether mammals, birds, amphibians and fish are monophyletic.

 

 

 

 

Sample Solution

on Sparks Street.” This demise is huge as in a letter “Woman Agnes MacDonald, the head of the state’s significant other… ‘McGee is killed.. lying in the road.. shot through the head.” Thomas McGee was an extraordinary public speaker, and profoundly clever figure who assumed a part Canadian history similar to the casualty of one of the principal political deaths throughout the entire existence of the country.

 

While contemplating notorious Canadian verifiable figures, one name that variables into the account of Canada is Thomas D’Arcy McGee. As student of history T.P Slattery makes sense of “Thomas D’Arcy McGee was brought into the world on Wednesday, April 13, 1825, in Carlingford Ireland on the Rosstrevor coast.” Thomas was raised by guardians “James McGee and Dorcas Catherine Morgan.” Carlingford would simply be McGee’s most memorable home as “When D’Arcy was eight, the family moved south to Wexford.” It was unfortunately during this time that “[Mcgee’s] mother was the casualty of a mishap and kicked the bucket on August 22, 1833. This was a weighty blow.” Thomas D’Arcy McGee was an Irish conceived resident who early on lost a focal figure in his life.

 

The significance Thomas D’Arcy McGee’s mom had on his life was impacting him on his philosophical convictions. One component of impact was a nationalistic conviction as Alexander Brady states “she was a lady who valued the memory of her dad’s embrace of the public reason and saved all his embrace of the public reason and protected all his public enthusiasms which she carefully took care of to her child.” McGee likewise fostered his insight on Irish writing from his mom, as Brady states “She was keen on the old Irish fantasies in general and customs and verse, and these she connected with her [son].” Thomas D’Arcy Mcgee’s patriot belief systems were impacted upon him early on, and that drove McGee to turn into “a vigorous romantic for the ethnicity of his country.”

 

Thomas D’Arcy McGee was an exceptionally smart human since early on. T.P Slattery in his novel states “A fence head master, named Michael Donnelly, helped him alongside his books.” Donnelly was a coach figure to McGee as he helped him concerning his tutoring. When gotten some information about McGee as an intellectual, Donnelly answered expressing that McGee was “the most brilliant researcher I at any point educated.” Thomas D’Arcy McGee was likewise an extraordinary public speaker. As T.P Slattery states “In Wexford, D’Arcy had an innocent snapshot of win when he gave a discourse before the Juvenile Temperance society, and Father Matthew, who turned out to be there, arrived at over and disheveled his hair.” Author Alexander Brady writes concerning McGee’s exhibition that it was “conveyed before the general public an entrancing discourse, on which he got the generous congrats… This was [Mcgee’s] first open discourse.” Thomas D’Arcy McGee was an extremely extraordinary person with an elevated degree of knowledge and a gift for public talking both recognizable early on.

 

Not a long lasting resident in Ireland, Thomas D’Arcy McGee continued on in to one more section in his life. There were different reasons that prompted McGee leaving Ireland, one of which being that “Mcgee’s dad had hitched once more, and the stepmother was not famous with the youngsters.” Another explanation of McGee moving needed to manage the monetary real factors of Ireland as made sense of by Alexander Brady “The financial design of Irish society was infected. Roughly 7,000,000 were pointlessly trying to wring a lean means from the land, and many thousands were nearly starvation.” With that data as a primary concern Robin Burns makes sense of on biographi.ca that “D’Arcy McGee left for North America in 1842, one of very nearly 93000 Irishmen who crossed the Atlantic that year.” Thomas set out from Ireland “on April seventh McGee [who] was not yet seventeen… with his sister Dorcas to proceed to live with their auntie, in Providence Rhode Island.” Thomas D’Arcy McGee had quite recently set out on another part in his life

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