Download Jurassic Park" Dinosaur DNA Analysis In 1990, Michael Crichton

Homework #2
Name: ____________________________
Jurassic Park" Dinosaur DNA Analysis
In 1990, Michael Crichton published the book "Jurassic Park" about the resurrection of dinosaurs using the
blood from the stomachs of insects which had been encased in tree sap, later turned into the mineral, amber.
At one point in the book, Dr. Henry Wu is asked to explain some of DNA techniques used in reconstructing the
extinct dinosaur genomes. Dr. Wu describes the use of restriction enzymes and how the fragmented pieces of
dinosaur DNA can be spliced together with these enzymes. He also alludes to the fact that they don't have the
entire genome but that they "fill in the gaps" with modern day frog DNA. At one point during his discussion he
points to a computer screen and says "Here you see the actual structure of a small fragment of dinosaur DNA."
The DNA sequence Dr. Wu refers to is on page 103 of the book Jurassic Park. In 1992, Dr. Mark Boguski (a
scientist at NCBI) entered this sequence into a text editor and searched all of the known DNA sequences at the
time. (In 1992 user friendly interfaces at NCBI and BLAST were under development).
Mark wrote up his findings and submitted a
manuscript to the journal BioTechniques, as
a joke.
His manuscript was accepted and published,
no joke.
Boguski, M.S. A Molecular Biologist Visits
Jurassic Park. (1992) BioTechniques
12(5):668‐669
You will reproduce this experiment using BLAST. The DNA sequence published in the novel Jurassic Park can be
found on the Molecular Biology course website under Problem Set 2. Copy the sequence and do a standard
BLAST search. http://www.ncbi.nlm.nih.gov/BLAST/ chose nucleotide BLAST. Change the “database” search to:
“non‐human, non‐mouse ESTs”. (Sorry, NCBI has since updated its default search to “human genomic” – how
anthropocentric of them!)
What is the best “hit” to your search for the “putative Dinosaur DNA”?
Mark Boguski’s published article was brought to Crichton's attention. In his second book, "The Lost World",
Mr. Crichton used Mark as a consultant. Mark decided to play a trick on Crichton and it went undetected. The
DNA sequence that Mark gave Crichton for the book “The Lost World” can be accessed from our course
website under Problem set 2.
Copy the LOST WORLD PROTEIN sequence and do a BLAST with a twist at NCBI.
Go to http://www.ncbi.nlm.nih.gov/BLAST/ Under the “Basic BLAST” search option, choose “protein BLAST”.
This will do a protein search and alignment. Do the BLAST search for the “Lost World” protein sequence.
What is the best “hit” to your search for the Lost World DNA? List both the gene and species?
What is the common name of this species? Do you think this is a closer relative to a dinosaur than the hit
retrieved from the first search with the “putative Dinosaur DNA”? Why?
Look carefully at the alignment from the protein BLAST you just did. Scroll down to the first alignment which
you will find after the “Graphic Summary” and “Descriptive Section”. Mark embedded a secret message
contained in the query sequence where the subject sequence has gaps (represented by dashes ‐‐‐).
What is his message?
Strange but true….some interesting cloning developments
In October 2006, researchers in Korea were able to take nuclear genomic DNA from a Siberian tiger skin cell
and implant it into an enucleated oocyte from a domestic pig. Surprisingly, multi‐celled embryos developed in
vitro (Figure shown below).
The goal of their study was to find in vitro conditions that promote growth of embryos cloned from the
nuclear DNA of the Siberian tiger. Another goal of interspecies nuclear transfer studies is to identify an animal
model which might be useful in carrying an endangered animal to term.
Although the possibility of a pig giving birth to a Siberian tiger seems extreme, scientists have been able to do
interspecies cloning in two other cases as explained on the following pages.
In 2001, Scientists used oocytes of cattle (Bos taurus) to clone the Gaur (Bos gaurus). A pregnancy was
produced, and one Gaur was born. This Gaur (shown below) died at 2 days of age of clostridial enteritis, a
bacterial infection that is almost universally fatal in newborn animals. Nevertheless, this research showed it
possible to have one species carry a cloned animal from another species to term.
In 2003, Scientists in San Diego created the first healthy clone of an endangered species (photo shown below).
Interestingly, the clone was created using DNA from a skin cell taken from a captive Banteng (Bos javanicus)
before it died in 1980. After 23 years, the cell was unfrozen and its nucleus placed into an enucleated
domestic cow (Bos taurus) oocyte. Scientists implanted the reconstituted embryo into a domesticated cow
and the baby Banteng was born after a standard gestation period.
Similar work has also been done with sheep. For example, the Mouflon (Ovis orientalis musimon) is found only
in Sardinia, Corsica, and Cyprus. Fewer than 1000 mature individuals remain in the wild.
Download the article by Loi et al. (Nature Biotechnology) from the course website and answer the questions
on the following page:
Where did the authors obtain the mouflon DNA?
Why do you suppose the authors had to have approval from the Sardinian Environmental Protection
Council?
Do you think their use of tissue from deceased animals was the best approach?
What is a “granulosa” cell?
Based on the author’s use of this cell do you think a granulosa cell is haploid or diploid?
Is a granulose cell a stem cell or a differentiated cell?
What species of animal was used to provide the enucleated oocyte?
What exactly is an “enucleated oocyte”?
How many oocytes were injected with mouflon nuclear DNA?
How many embryos developed into blastocysts in vitro?
How many domestic sheep were the blastocysts partitioned between for implantation?
How many of these blastocysts developed to full term (i.e. a baby mouflon was born)?
What are TWO of the reasons the authors propose could lead to the low number of viable offspring in such
interspecies cloning attempts?
1.
2.
In their discussion, the authors explain how cloning involving nuclear transfer does not produce true clones in
the strictest sense. Offspring produced this way will have identical nuclear DNA to that of the nuclear DNA
donor, however, there is another pool of DNA within a cell: mitochondria.
What is the genetic makeup (genius species) of the mouflon offspring produced in this study?
Nuclear DNA: __________________
mtDNA: _______________________
Are the microsatellites shown in Figure 2 from loci on chromosomes or mitochondria?
Why did the authors include the data depicted in Figure 2 in this paper?