Question

• What genes (or kind of genes) will you focus on in your investigative research? Provide 2-3 reasons for your choice of these gene/s.
• Starting with the bone sample itself, what methods will you use to get DNA that you can sequence?
• Which “ingredients” in your lab reactions will determine which gene or genes are copied? How is it that these ingredients are able to target a specific gene?
• What method will you use to see if your efforts to copy the DNA have succeeded? In briefest terms, how does this method work?

In 2016, scientists working at an important archeological site near Vero beach, Florida discovered a well-preserved bone that they believe to be 14,000 year old. The archeologists believe this bone came from an extinct species of bison (Bison antiquus) which used to live in the southeastern US. Now, let’s imagine you feel this hypothesis is wrong. Instead, you hypothesize that the bone came from a cow name Belinda who disappeared from a nearby ranch last year. Briefly explain how you will use genetics to test your hypothesis.

PLEASE take note: Your final step in this study will be to compare DNA sequences you obtain from the archeological sample with DNA sequences from other sources (including sequences from both cows and bison). These comparisons will utilize some computational techniques that we will learn about later this semester in lecture and lab. So for now, I am only asking you to tell me how you will get the DNA sequence from the ‘bone of contention’ that was found at Vero beach. To do this, please answer these questions: (1-3 sentences per each question)

What genes (or kind of genes) will you focus on in your investigative research? Provide 2-3 reasons for your choice of these gene/s.

Starting with the bone sample itself, what methods will you use to get DNA that you can sequence?

Which “ingredients” in your lab reactions will determine which gene or genes are copied? How is it that these ingredients are able to target a specific gene?

What method will you use to see if your efforts to copy the DNA have succeeded? In briefest terms, how does this method work?

Question 2: (33 points) You learn that SuperGMOpets is in the process of commercializing a new kind of pet, called the yawncat. These animals’ R-locus regulates tail patterning. The dominant allele (R) causes a solid tail, and the recessive allele (r) results in white striping on the tail color. A different gene at the B-locus controls yawncat coat coloration (including the tail color, with or without the white striping). Here, the brown coat color allele (B) is dominant to the black allele (b). However, B locus coat color genes can only be expressed if the animal has an mm genotype at a third gene locus called M. Animals that are M- (i.e. yawncats with Mm or MM genotypes at the m locus) are yellow, regardless of which allele from the B-locus is present.

Now, let’s say that a mating between a yellow male yawncat with a solid tail and a brown female yawncat with a solid tail produce 16 offspring with the following tail phenotypes: six solid yellow, two striped yellow, three solid black, one striped black, three solid brown, and one striped brown.

What are the most likely genotypes (at all three loci) of the male and female parents? Explain the strategy used to determine the genotypes.

Which phenotype is controlled by epistatic effects in the yawncat?

Question 3: (33 points) Name three mechanisms for non-Medellian inheritance, and explain each of them in 1-3 sentences. Next, chose one of these mechanisms and find an example of a published research study that demonstrates its occurrence in nature (humans, or other animals, or plants, etc..). Describe it very briefly, mentioning a) the phenotype that was shown to be affected by your chosen mechanism of non-Mendellian inheritance, and b) the citation for the study you chose. You may use Google Scholar, PubMed, or other databases to conduct this search.

Answer 1

ANSWER 1 :-

1. Taking into consideration the points detailed in the paragraph, the fossil specimen is stated to be 14000 years old. Now, we are able to find two types of DNA in the cell more specifically related to archaeological analysis. One is the genomic DNA which usually tends to denature at a faster pace after death of the organism and is from both the parents in origin. Other one is the mitochondria DNA which is localized in the cell organelle called mitochondria and can replicate on its own (self-autonomous). Taking into consideration many copies of mitochondrial DNA would be seen as compared to the genomic DNA, it would be preferred to extract the mt-DNA to test the hypothesis. To specifically mention a gene is not possible as the functional aspect wont be active. Indeed, if the sequence of the extinct bison is known from dataset, Variable number tandem repeats (VNTR) and sequence tagged elements can be used to identify the variations and changes that have occured and their similarities and differences if present as we are dealing with mt-DNA which is sensitive to mutations.
2. mt-DNA can be eluted as a part of the cellular content by means of performing cell lysis by means of using SDS or detergents. Although, in case of bones, the upper layer is removed and fine powder is made which is then used to separate DNA. A silica based adsorption column is made and as silica ions carry partial negative charges, the binding between negatively charged DNA and the silica can be initiated only if the pH of the buffer that is used to separate the contents is less than the pKa value of the silica associated ions. This mediate interaction between the DNA and silica and other components can be washed out. The elution buffer with low salt concentration is then used to elute the DNA. This DNA contains both genomic and mt-DNA elements and for more specific isolation, mt-DNA isolation kits are available based on separating the DNA (genomic) by using cytosolic extraction buffer followed by centrifugation and treatment with mitochondrial lysis buffer to elute the mitochondrial DNA content from the mixture which is subjected to centrifugation to finally isolated the required DNA.
3. It should be taken into consideration that PCR process plays a vital role in determination of sequences as primers specifically designed to target a known site can be used to form many copies of the sequence of interest prior to restriction digestion. So, the basic strategy would be to implement restriction digestion depending upon the gene sequence known. To specifically isolated a gene of interest, the sequence can be labelled with a fluorophore by using nucleotide analogs which acts in the manner of anitgen-antibody interaction. Specifically, I cannot mention a gene of interest as it depends upon various factors including study of genes present during developmental stages or genes involved in processes of aerobic respiration as associated with mitochondria.
4. First of all, if the DNA is isolated, it is very important to specify it isolation by means of performing electrophoresis which helps to evaluate the fragment sizes and availability of any irregularities in terms of structures. In certain cases, DNA sequencing is carried out if unknown sequences are being sorted out. But in this case, as the DNA sequence is known, it needs to be sequenced in order to carry out comparative analysis with respect to similarities with the extinct bull genes. This will give an estimation regarding its relatedness. Specifically as stated above, certain regions will remain similar or may not show variations which can be used to characterize the relatedness. To check whether the DNA has been properly isolated, one can depend on electrophoresis and PCR analysis as a core tool to indicate its authenticity in terms of DNA isolation.

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