1. Your cousin complains to you that every morning when he steps outside his doo
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1. Your cousin complains to you that every morning when he steps outside his door there is a smelly "deposit" left on his front steps by one his neighbor's dogs. However, he doesn't know which local canine is the culprit: Rover, the cocker spaniel from next door: Spot from across the street, who is suspected of being Rover's illegitimate son, or Max, the pitbull from down the block that really just doesn't like your cousin. Luckily, being up to date on all genetic developments, you tell your cousin about a new company that can help him with his problem. The company "Poo Prints", for a small fee, will perform DNA fingerprints on neighborhood dogs and "samples" they may have left behind so the culprit can be identified. You help your cousin collect saliva from each of the suspected dogs, but you make him collect some of the fecal matter left on his front steps, and you send them to Poo Prints. The results are shown below Smelly Rover Spot Max sample (A) Which dog is the culprit that is leaving behind the fecal matter on your cousin's steps? Explain. (0.5 pts. total) (B) For an additional fee, Poo Prints will "genotype" individual dogs for up to 13 different STR loci by using PCR to produce DNA fragments of different sizes that can be viewed using gel electrophoresis What is an STR and how can they be used to "genotype" an individual? (0.5 pts.) Suppose you had each of the three dogs described above, along with Snookums, Spot's mother genotyped in this manner, DNA analysis for three different STRs produces products of the following sizes STR Loci PEZ01 Sample DCB 2010 UIC B2079 ITs. 105. 125, 140 Snookums 220, 230 Rover l 15, 135 230, 249 Spot 125, 135 230 78, 95 Max 135 220, 240 105, 110Explanation / Answer
i.
(A) Since the DNA pattern of the smelly sample matches with the Max’s DNA fingerprint, the pitbull from down the block, the sample belongs to Max, and the culprit is Max.
(B) STR Genotyping: Amplified fragment length polymorphisms can be divided into two categories: Long Tandem Repeats (LTRs) and Short Tandem Repeats (STRs). Both LTRs and STRs can be amplified using the polymerase chain reaction. One of the advantages of analyzing PCR-based variable number tandem repeat systems is that individual alleles can be resolved into more discrete fragments than with RFLP analysis. Discrete alleles enable phenotype determination by reference to allelic ladders in adjacent lanes of the gel or, in the case of some fluorescent-based detection systems, by reference to an internal lane standard
Short Tandem Repeats (STRs) are efficient tools for mapping specific traits or to follow the flow of genetic material in a population. The technology is based on the presence of short tracks of di, tri, tetra or penta nucleotide repeats which are common in the genomes of eukaryotic organisms. Dinucleotide repeats dominate, (CA)n repeats are most frequent, followed by (AT)n, (GA)n, and (GC)n, the last type or repeat being rare. Large majority of simple repeats are embedded in noncoding DNA. These short tracks (5-10 repeating units) are faithfully transmitted through sexual reproduction but are often highly polymorphic within a population.
Genomic DNA is purified, and the short tandem repeat (STR) regions of interest are amplified using the polymerase chain reaction (PCR). The amplification products, generally less than 500bp in size, are analyzed on a denaturing polyacrylamide gel. Allelic ladders containing fragments of the same size as several or all known alleles are run on the gel alongside the amplified samples. Comparison of sample and allelic ladders allows easy interpretation of amplified alleles. After electrophoresis, alleles are detected by silver staining, fluorescent detection or the use of radioactivity.
ii. Given is the STR size of three different loci PEZ01, DCB2010 and UCB2079 from Rover, Spot, Max, and Spot’s mother. It is believed that STRs are sexually transmitted, but within a population, only one loci will be transmitted to the offspring either from maternal or paternal side. Spot has two different sizes of loci PEZ01, 125 and 135, its one of the STR matches with that of Snookums’s STR, but it is not possible to decide the father of Spot with this STR because both Rover and Max had a 135 sized STR.
iii. Spot also exhibited the STRs of loci DCB2010 of 230 size which matches with the same loci of Rover, and UCB2079 of 78, 95 kDa, which matches one of the UCB2079 loci of Rover, 95. Therefore, the data indicates that the Rover is the father of Spot.
iv. Some of the loci may be lost during crossing-over during meiosis i.e., during formation of sperm or ovum. Thus it can be expected the existence of one or no product for the same loci in an individual.
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