Vanessa+Decker


 * [[image:http://ldcollins.com/ld-images/header-image-dna2.jpg width="1004" height="203"]] ||


 * = Cloning with Bacterial Plasmids = ||



**Describe** : Bacteria cells contain plasmids, which are DNA molecules that replicate separately from the bacterial chromosome and are relatively small. Scientists can extract these plasmids and insert a segment of foreign DNA in the plasmid molecule, and then insert the molecule back into the bacterial cell, where it is replicated along with the bacterial DNA.


 * Analyze :** The new DNA that is inserted into the plasmid comes from the DNA of a different organism, forming recombinant DNA when it is added. When these new genes are expressed in the bacteria cell, the organism is allowed to function in a new way, and can be applied in many different ways.

[|Medicinal Uses for Genetic Recombination]
 * Apply :** When genes are inserted into other organisms, the results can include pest-resistant plants such as corn,and bacteria that consume oil spills. The protein products that are harvested when genes are translated can also be used for medications and treatments such as insulin and artificial hormone production. Here is an article that provides a lot of great examples of application for genetic recombination in medicine.


 * Synthesize :** This is like putting chocolate chips in cookies. They're still cookies, just with a new chocolately twist! Just like the tobacco plant in our textbook, where its still a tobacco plant, except it took on the new characterisitic of possessing the ability to glow.

**Argue** : Bacterial gene cloning has had many positive results in science, with low costs and fast results. This article states that bacteria can produce a billion clones in only 11 hours, making it a great source for research and application. [|Article on Cloning]

= Nucleic Acid Hybridization =

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[|http://www.molecular-beacons.org/download/antony,jbsd01(19)497.pdf]
 * Describe :** Thousands of clones are added to a special nylon membrane. A set of these membranes can be used to screen for a specific gene with a DNA strand called a probe. The membrane is immersed in a solution that contains probe molecules, and when the probe DNA binds with the gene being searched for, a hybrid is formed. Any single stranded nucleic acids can be used, because all they need to do is bind with one another. A film is laid on top of the membrane and the film is stained where the hybrid is located, showing you where the gene is that you are looking for!=====

**Apply** : This is one of the procedures needed during cloning, so that scientists can identify the clones that carry the genes they are looking for. It can be used anytime scientists need to locate a certain gene, like when someone wants to know if they carry a disease that runs in their family.
 * Analyze :** This process is used to locate certain genes when cloning. You need many different materials,like film, nylon, and probe DNA (or RNA can be used).

**Synthesize** : This reminds me of using a metal detector to find something hidden.

**Argue** : This is a great experiment to do if it is voluntary. For instance, if you were a potential carrier for the alzheimer's gene, you might not want to know, and a court case should not be able to make you get one. Also, there are a lot of ethical arguments surrounding whether a mother should get rid of a baby that has tested positive for certain genetic defects.

= Genomic Library =

**Describe** : This is a large number of bacterial or phage clones that contain recombinants of a certain gene. They are stored in a 'multi-well' plastic plate.
This helps scientists organize large numbers of different gene sequences for further research and can be used to screen for genes (nucleic acid hybridization!). A genomic library is the result of a mixture of fragments of an organism, not just the cloning of a single targeted gene. This makes for high levels of variety and so genomic libraries are needed to organize everything!

** Apply :** This is used to organize and store clones so scientists can research different genes and locate the ones they are looking for.
**Analyze** : A genomic library is made when many different genes are inserted into plasmids and DNA ligase is added to seal the DNA fragments. These plasmids are taken up by bacteria which can reproduce and the different clones can be organized in the genomic library.

**Synthesize** : This is a lot like a dictionary: just like we have sequences of letters that we can organize for their different possible combinations, genes are made up of nucleotide sequences that we can organize in the a genomic library and analyze for their 'meanings' or results of certain genes in the bacteria!

**Argue** : This is really important because if we have no organization method, then it would be very hard to analyze the results of many different gene types and combinations in a bacterial cell. []

= Polymerase Chain Reaction =

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 * Describe :** A short, specific segment of DNA is rapidly replicated outside of a host cell. After many replications, 99.99% of DNA strands match the starting host strand. Its much more precise and efficient than making a genomic library.=====

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**Analyze** : A mixture containing the targeted DNA strand is heated to separate the DNA strands from each other. After it is cooled, the primers from hydrogen bonds, and DNA polymerase matches the base sequences (polymerase that withstands the high temperatures is found in archaebacteria, pg. 404 in the textbook). The new double stranded DNA strand can then be reheated and replicated again. When is process is repeated many times over, then the DNA strands identical to the first far outweigh all the others. Here's a great activity to help you visualize the process:===== []

**Apply** : This can be used to research the remains of organisms that are thousands of years old, or to amplify the DNA bits taken from a crime scene so the owner can be located and further testing can be done.

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 * Synthesize :** This reminds me of the story where the little boy did something honorable and the emperor told him he could have anything he wanted so he a grain of rice on a chess square and told him to double the number of grains on each additional square, so the rice multiplied until the boy became a very rich man. (A little random, but that's what it reminds me of because the strand of DNA get doubled as exponentially as the rice.)=====

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**Argue** : I like really like this method of gene replication because its fast, efficient, and can target a single gene directly. Its definitely important when you only have a small piece of DNA collected from a crime scene and it doesn't have any ethical complications.=====

= Gel Electrophoresis =

**Describe** : DNA molecules are separated based on size, electrical charge, or other physical properties.
**Analyze** : Molecules travel through a gel, the negatively charged particles attracted by the positive charge on the other side of the field. Since the smaller particles can move faster, turning off the current reveals bands like the one in the picture, where the particles are visibly separated after the dye is added. The cluster of DNA molecules in each band contains strand that are all the same length.

**Apply** : Any kind of a sample, such as a blood or urine sample, can be placed next to a normal sample and analyzed. If the resulting bands are different, then abnormalities are detected and further testing can be done. This is an easy, efficient method for testing 'all of the above' at the same time to see if any abnormalities at all are present in the sample. Vaccines can also be purified and processed through electrophoresis, making it an extreme contributor to the health of society. [|Source]


 * Synthesize :** This is a lot like a car race. When two cars are put to the test, its often the lighter car that comes out ahead, because it tends to be smaller! After the race is over, its easy to tell that there's a difference between the two cars and they can be compared and analyzed.

**Argue** : One advantage of this is its simplicity, and how quickly results can be obtained. The results however, often have to be analyzed further, so its not completely precise in its diagnosis.

= Southern Blotting =

**Design** : Nucleic acid hybridization and gel electrophoresis are combined so that certain genes can be separated and located in the DNA.
**Analyze** : This is a five step procedure: 1. DNA chromosomes are cut up by the same restriction enzymes 2. The segments are separated by electrophoresis 3. The stained bands are transferred to a membrane 4. The radioactive probe is added for hybridization 5. A film is laid over the blot and the gene is located by the stained bands :) yay! [|Great Animation on Southern Blotting!]

**Apply** : This can be used to determine if people are carriers of genetic diseases, or to test if an inserted portion of DNA has truly been incorporated into the genome of an organism! It can also help scientists determine the molecular weight of a fragment or measure different samples relatively. [|This Link Has a Lot of Information But You Have to Scroll Down a Lot]

**Synthesize** : This makes me think of the indicator solution used in a titration and how it shows that a certain substance is present in a certain amount. Like the indicator shows the presence of a certain substance, Southern Blotting shows the presence of a certain gene!

**Argue** : I love how this process can combine the more simple steps that we've learned to give more information than the other procedures could have done separately. I think its really cool, too, how certain genes can be located.

= Microarrays =

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**Design** : A collection of DNA segments that are grouped and placed on a glass plate in a grid format. Each dot, or DNA cluster, represents a gene. The entire grid represents the entire genome of an organism.===== **Analyze** : A microarray can be used to show levels of gene expression on thousands of genes at a time through this process: 1. Isolate the mRNa from the tissue sample. 2. Use reverse transcriptase to cDNA by using fluorescently labeled nucleotides. 3. Apply the mixture to a microarray, where the cDNA will hybridize with complementary strands. 4. Rinse of excess solution and scan for fluorescence. Each fluorescent spot represents a gene being expressed. media type="youtube" key="VNsThMNjKhM" height="315" width="420"

**Apply** : Thousands of genes can be tested for levels of expression at the same time under different situations such as under disease infection, different levels of development, or in different environmental conditions. [|Awesome Virtual Lab!]


 * Synthesize **: Most people compare this to a computer chip, nicknaming it a DNA chip!


 * Argue **: This is a very efficient, extremely important tool in a lot of different experiments involving genes and their expression. I don't know what science would do without it!

= Plant Cloning =

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 * Design **: A new plant is produced that is identical to the original plant. This includes the same growth habit, disease resistance, physical characteristics, and range of yield. And, just like the bacteria we studied, recombinant plasmids can be inserted to give the plant new characterisitics, this like tobacco plant.=====
 * Analyze **: Somatic cells of a plant can be added to a test tube mixture and a single cell can be isolated and will divide to form a mature adult plant when cultured on agar medium and planted into the soil.


 * Apply **: This can be used to reproduce plants with special characterisitics, like disease resistance, and for some plants its the only practical way to reproduce some plants, like orchids, for which it takes all season to reproduce.


 * Synthesize **: If you combine this process with the process of producing transgenic plants, you could introduce a whole new population of plants that carry a new function, which could combat issues like world hunger.

[]
 * Argue **: This is advantageous for some plants because they're population can be renewed quickly after danger of extinction, and the process is faster and less expensive than seeds, but there is no room for genetic diversity among a population.

= Animal Cloning = **Design** : A genetically identical offspring is produced from an organism by nuclear transplantation. media type="youtube" key="tJmoT7xbrvw" height="315" width="420" **Analyze** : 1. The nucleus of a somatic cell is fused with an denucleated cell 2. The cell is grown in culture, growing into an early embryo 3. The embryo is implanted in the uterus of a third mother 4. The embryo develops and becomes a genetically identical individual to the somatic cell donor.

**Apply** : An animal that has been genetically modified to produce a certain protein could be cloned so that more medically-utilized protein could be produced, or cloning could save a species from extinction. Also, cloning has high potential in treating human diseases when stem cells are used, but since these cells come from human embryos, controversy is encountered. [|Cloning Answers Sheet]

**Synthesize** : Combining cloning with tools like retroviruses and gene recombination might someday be able to help with treating diseases, even though recent attempts have been unsuccessful.

**Argue** : Animal cloning is a hotly debated issue, and for good reasons. While scientists argue that many medical treatments could be developed with further research, others argue that their efforts could backfire, and result in the end of the human race because a bad mutation now could turn out to be a life-saving on later, like in the case of sickle-cell alleles. While I have high hopes for the future of using retroviruses and dedifferentiating cells, and I hope that these new methods can be used someday to benefit cancer patients.

= Restriction Fragment Length Polymorphism =

** Design **: Different lengths of restriction fragments are produced by restriction enzymes because of a difference in nucleotide sequence.

 * Analyze **: In sickle-cell disease patient, there is a single nucleotide that differs from the normal one, often indicating the presence of a disease causing allele. When restriction enzymes cut up the DNA, different fragment lengths are shown through electrophoresis, and variation in fragment length, or RFLP, serves as an indicator for a certain disease.
 * Apply **: RFLPs alert scientists that a certain disease causing allele is present, identifying genetic disease carriers. If the fragment lengths have the same electrophoresis pattern as a known disease, then the patient can be diagnosed if necessary.

[|Restriction Fragment Length Polymorphism]
 * Synthesize **: RFLPs can be further used to locate certain genes when southern blotting is used. Also, they can be used in paternity tests and forensics instead of gene sequencing.


 * Argue **: This is important because it often allows scientists to skip DNA sequencing to pinpoint certain individuals.

= Gene Therapy =

** Design **: New genes are introduced into an individual with hopes that it will cure the genetically-based disease of the afflicted individual.
[|Article on Gene Therapy] [][|Recent Advances]
 * Analyze **: Gene's are inserted into the retrovirus and injected into the bone marrow. The virus infects the cells and the new DNA causes them to make a new protein-one that is needed by the body.
 * Apply **: This process can be used to treat diseases like diabetes, in which patients fail to produce insulin. There are many hopes that it will someday be able to cure cancer, Parkinson's disease, Huntington's, and many other genetic diseases.

**Synthesize**: I want to see this combined with animal cloning to produce a new liver or kidney that will develop while its still inside of you! That would be nuts.

**Argue** : I really support this type of research because it seems the only way to change the genetic mutations that cause certain diseases. It also seems to have the most potential for curing cancer.

= **Transgenic Animals (Genetically Modified Organisms)** = **Design**: An animal that carries foreign DNA that was directed inserted into its genome, and now has a new function because of it. []



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**Analyze:** Gene's are incorporated into the animal's DNA during early embryonic development. The embryo is implanted into the uterus of a mother, and the animal expresses the implanted genes when it is born! A retrovirus can also be used to incorporate these genes. =====

**Apply:**

 * ===== Animal's that produce proteins for human vaccine production =====
 * Mice have been infected with human genetic diseases so they can be researched to find a cure
 * Animals that produce better quality materials (like wool), better breeding, or disease resistance
 * The numbers of animals used for research has decreased

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**Synthesize:** I'm really hoping the the disease models produced can lead to a cure in cancer, and many other diseases. If one animal's life has so much significance in curing the diseases of thousands of humans, that would be enough justification for me to have diseases injected into animal's for research. =====

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**Argue:** While these methods are really cool and have high potential, I do worry about what will happen when humans begin having too much power with genetic manipulation. What if a mother wants to engineer a perfect baby? If people began doing this, then it would only be the rich who would dominate competition in schools and careers. What if people began hiring only those with good genetic profiles? What if genetic profiles became no longer reliable because people could develop the power to change it? There are a lot of questions that have very reasonable ethical concerns and I hope that having so much control over the genome doesn't backfire on humans. =====

=** Transgenic Plants (Genetically Modified Organisms) **=

** Apply: **
[] []
 * ===== Improved flavor =====
 * Pest and disease resistance
 * Oral vaccine production
 * Highly increased nutritional value


 * Synthesize: ** I would want to try putting plant genes into animal genomes to see what different types of charactistics could be developed. The ability of a tobacco plant to glow was pretty cool, and I would like to see regeneration in animals!

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I have no objections to this method, since eating transgenic plants has not shown to have a harmful impact on humans. These methods have had only benefits, like producing rice with high Vitamin A value, and creating types of plants that farmers can grow without worrying about certain diseases or pests. Its improved our industry, and I can't wait to see what it does next :) ===== =** Genetic Profiles (DNA Forensic Testing) **=
 * Design: ** Tandem repeats are numbered so DNA can be matched with a certain individual.

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 * Analyze: ** Even though 99.99% of the human genome is identical in every person, there are certain small sequences that make it possible for DNA to serve as a fingerprint for genetic testing. These short repeated nucleotide sequences are called tandem repeats and can be counted, making it possible to match a set of tandem repeat numbers to an individual. =====

** Apply: **

 * ===== Match child with parent (paternal testing) =====
 * Match crime scene evidence with suspect (Forensics)

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**Synthesize:** I would like to see this used for when children have been placed into adoption they can still find their parents because of it. Maybe someday everyone's information could be recorded at birth so anytime there's a crime scene they can be located right away instead of testing everyone who might have been involved after the fact. Or when they go missing and a body is found, the person can be indentified even if there is only a trace of them. =====

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 * Argue: ** I love this method because it has worked to free many criminals during The Innocence Project and also to help indentify people after 9-11. Its value has been proved many times over and it has given us a way to be more sure that justice has been done after someone is declared guilty based on DNA evidence. =====