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=**[|**Gene Cloning]****[|with Bacterial Plasmids**]**=
 * Described:** Every bacteria cell has two types of DNA: bacterial DNA and plasmids, and gene cloning involves the manipulation of these bacterial plasmids. Plasmids are small circular forms of DNA which are separate from the normal DNA of the cell.


 * Analyzed:** In the process of gene cloning, the plasmids open at their origins of replication to form sticky ends which are the ends of the opened circle. The desired genes are then inserted into this open area to create new plasmids with a completely different genetic structure.


 * Applied:** The alteration of bacterial plasmids provide substantial health benefits such as the use of bacteria to create and harvest human insulin. With this process pharmaceutical companies can create highly specialized products with the exact genetic structure needed.


 * Synthesized:** In my opinion, genetic cloning is similar to highly specialized farming. Just as a farmer will create specific conditions to produce specific goods, a scientist will alter the conditions of a bacteria cell and its environment in order to create specific products.


 * Advocated:** Although genetic cloning raises serious ethical and moral issues, the manipulation of bacterial plasmids is entirely legitimate. The fundamental difference—in my opinion—is the life of bacteria is inherently different than the life of an autonomous creature. Bacteria are not self-aware;thus, the manipulation of them is not immoral. Altering the genetic makeup of bacteria provides the benefits of highly tailored genetic products without violating the inherent rights of sovereign organisms.



Sources General Information: http://www.sumanasinc.com/webcontent/animations/content/plasmidcloning.html Picture: http://wikipremed.com/image_science_archive_th/040202_th/268350_320px-Plasmid_%28english%29.svg_68.jpg

=**__Genomic Library__**﻿ = **Described:** It consists of the entire genome of an organism so they are very complex. The size varies however, depending on the length of the genome being cloned. Within it are bacterial clones which are shown above and phage clones. Phage clones appear to look like keys and contain recombinant DNA.

**Analyzed:** It is made by cloning the whole genome of an organism and is a collection of many bacterial or phage clones. Genomic Libraries are made up of different cloning vectors such as plasmids in the form of bacterial clones and phage clones.


 * Applied:** These libraries can be made by researchers, commercial sources, or a sequencing center and then given to scientists to aid them in using a probe for further study and analysis to learn more about particular areas of interest in the genome.

It is packed full of all the information on a certain subject just like the Library is packed full of the whole genome of an organism. Essentially the "library" is actually more like a book than a library.
 * Synthesized**: I would compare a Genomic Library to a reference book.

libraries. All the benefits inherent within the use of them are countless. They can substantially aid scientists when finding new uses for bacterial clones.
 * Advocated:** There seems to be no negative affects stemming from the use of genomic

Sources: http://www.wisegeek.com/what-is-a-genomic-library.htm and http://www.web-books.com/MoBio/Free/Ch9B.htm Picture: http://avonapbio.pbworks.com/w/page/9429274/Ch-20

=__Nucleic Acid Hybridization__= **Described:** Nucleic Acid Hybridization is when DNA forms a hydrogen bond that holds it together. With A connecting to T and C connecting to G. Hybridization takes place between two complementary DNA sequences, a single-stranded DNA and a complementary RNA, or two RNA sequ ences.

**Analyzed:** Nucleic acid hybridization can be used for many genetic experiments. It is used to detect specific complementary stands. Scientists use it to try to make a superior strand of DNA. If someone has a double helix where one strand is normal and the other is mutated, they will take the normal strand and combine it with another normal strand. This will take away the mutation allowing the person to be normal for that certain trait. .

**Applied:** Scientists take a double helix strand of DNA and denature it. They do this by heating the DNA to 100°C. This will cause the complementary base pairs to be disrupted. This causes the helix to be pushed apart from the two strands of DNA. This process is reversible as long as both str ands of DNA are kept at a temperature of 65°C. The process of reconnecting the two stands is called hybridization.

**Synthesized:** Nucleic Acid Hybridization is like PCR. PCR is the technique of making more copies of a gene. It is a lot like Nu cleic Acid Hybridization. It is just amplified to make many copies of a gene.

**Advocated:** In my opinion, Nucleic Acid Hybridization would be a very good thing, if perfected. It could help people will genetic disorders by helping to completely eliminate the mutated stand of DNA. Therefore, not only would it help the person with the disorder but it would stop it from being passed on.

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=__Polymerase Chain Reaction (PCR)__=
 * Described:** PCR is a process by which scientists can amplify certain areas of DNA for replication. The two DNA strands are heated until they separate and then cooled to allow the primers to hybridize to the DNA strands forming 2 new strands. This process can be repeated many times doubling the copies of DNA each time. This rapid procedure is very useful.


 * Analyzed:** There are many components of this process. The obvious one is the existing DNA strand. Other parts include the primers or new DNA that will be attached to the old DNA. Also taq polymerase and deoxyribonulceotides are parts of the process. The polymerase functions to elongate the DNA after the primers are put in place and the deoxyribonucleotides are what is put in place by the polymerase.


 * Applied:** There are many things that can be done with PCR. The main way it is used is to amplify very small amounts of DNA in order for scientists to have a far better understanding of certain diseases that humans can obtain. They are used in detecting infectious diseases in organisms and detecting variations and mutations in certain genes. PCR can also be used to determine how likely parents are to have a child with a certain disease or disorder.


 * Synthesized:** PCR reminds me of making copies of a specific page of a book on a copy machine. Just like in PCR where only a small portion of the DNA is replicated at a time, you can only copy one page of the book at a time. However, both of these processes can make mass amounts of that single piece of information in small amounts of time.


 * Advocated:** In my opinion this process is very useful and I must stand in favor of it. It allows scientists a unique opportunity to take the small molecule of DNA and replicate it many times quickly in order to learn more about it. This in turn is used to find out more about diseases and can help people live healthier lives. While the use of PCR to predict possible offspring is slightly controversial, I believe it is still a moral process because the child hasn't been conceived yet.

Sources: http://library.thinkquest.org/28599/analogies.htm http://www.nhlcyberfamily.org/tests/pcr.htm Picture: http://scienceblogs.com/insolence/2007/06/the_autism_omnibus_the_difference_betwee.php

=__Southern Blotting__ After clinking link, go to Southern Blot=
 * Described:** Southern blotting is a process that essentially works in combination with gel electrophoresis and nucleic acid hybridization. This is what actually lets scientists detect the bands that form during the process. A sheet called a membrane is placed over the solution and when it is pulled off the radioactivity causes the film to form an image by attracting complimentary bases.


 * Analyzed:** The process includes many steps. First a scientist must prepare the restriction fragments that will be tested. Next the gel electrophoresis takes place. Thenthe blot happens because the special membrane film pulls the DNA to the top because of the complimentary bases attraction.


 * Applied:** Southern blot can be very useful in identifying carriers of mutant alleles associated with genetic diseases. It has been a workhorse in the laboratory for many years. Recently it has sort of been supplanted with more efficient methods like PCR but it is still widely used to determine things in the laboratory.


 * Synthesized:** Southern blotting reminds me a procedure used in art class. When something needs to be traced it works to cover the backside of the paper will lead. Then you can tape it onto the paper you are tracing on and use a pen to go over the lines. The pen pushes down on certain parts and the lead is transferred to the other sheet of paper. In southern blotting the DNA is transferred onto the film and makes a pattern to show what alleles cause certain things.


 * Not Advocated:** While this process has been very useful in the past, most recently PCR has begun replacing this process. PCR is much more efficient because of the rate at which the process can be performed. This makes southern blotting kind of obsolete and therefore I would advocate different methods over it.

Sources: Campbell Reece Biology book, AP 8th edition http://www.bio.davidson.edu/courses/genomics/method/Southernblot.html Picture: http://www.molecularstation.com/dna/southern-blot/

=[|**Microarrys**]= ==
 * Described:** A microarry is technological tool which allows a scientist to analyze which genes are turn on (being expressed an turned into proteins) and which genes are turn (not being expressed and turned into proteins).


 * Analyzed:** In order to perform this experiment, a scientist must acquire a microarry which is generally purchased from a biological cooperation and is a base with thousands of DNA sequences attached to it. The scientist will then take two different types of cells from the specimen such as an eye and a liver sample or a healthy and cancerous cell apply a solution place them in a centrifuge and analyze the mRNA within the cell.


 * Applied:** Since a microarry has thousands of DNA sequences that attracts mRNA counterparts it is a tool that allows scientists to examine thousands of mRNA sequences in a short amount of time.


 * Synthesized:** The technology in a microarry can be enhanced with an expansion of available DNA sequences which would then increase the amount of mRNA sequences that could be studied at a particular time.


 * Advocated:** Microarrays is an effective tool for scientists to compare the genetic information of various cell. This process doesn't violate morals or ethics because it is simply expanding our knowledge. However, the information that it provides may provide us the knowledge for unethical and dangerous forms of biotechnology.


 * Sources:**
 * General Information:** http://learn.genetics.utah.edu/content/labs/microarray/
 * Picture:** http://www.dnamicroarray.net/image/Two-Color%20microarrays.jpg

=[|Gel Electrophoresis]=
 * Described:** Separates fragments of DNA, RNA, or protein molecules. It is a gel field that separates the fragments by what size they are.


 * Analyzed:** Gel electrophoresis is made up of a thicket of polymer fibers. This helps to slow down the larger molecules. The length of the molecule can show scientist the patterns of DNA sequence. These patterns can tell us many things about the molecule and the restriction enzyme being used. The patterns tell us if someone has or carries a certain gene. [[image:Gel_eletrophesis.jpg width="350" height="262" align="right"]]


 * Applied:** One application technique is restriction fragment analysis. This is when the DNA fragments cut by the restriction enzyme are sorted by gel electrophoresis. Once this process has taken place it yields band characteristics of the starting molecule and the restriction enzyme that was used. The smaller DNA molecule such as, virus or plasmid DNA, can be identified just by looking at their restriction fragment patterns. Restriction fragment analysis is a rapid way of providing information about DNA sequences.


 * Synthesized:** Gel electrophoresis is like The running back is small and fast, whereas the lineman is big. If both of the players were told to run down the field and see how far they could get in 10 seconds, the running back would go further. Just like in the gel the smaller pieces travel farther.


 * Advocated:** I think that Gel Electrophoresis is a very good thing. It causes no harm to the people that the DNA was taken from and can help uncover many things about a persons DNA. It can help us discover if someone DNA contains or carries a trait for a genetic inherited disease. It can even help detective resolve crimes through sample of DNA. The DNA is still in tact after it has been run through the cell so it can still be examined.


 * Sources:**http://www.dnalc.org/resources/animations/gelelectrophoresis.html
 * http://learn.genetics.utah.edu/content/labs/gel/ **
 * Picture:** http://www.molecularstation.com/images/agarose-gel-electrophoresis.jpg

= = =[|Animal Cloning]=
 * Described:** The process of animal cloning is taking a nucleus from a parent cell and inserting it into a unfertilized egg in order to create an exact replica of the parent animal.
 * Analyzed:** In order to perform animal cloning, a scientist must first acquire the nucleus of a parent and then insert it into an unfertilized that has had its nucleus removed. After this transition occurs, the cell is stimulated with either an electrical or chemical charge which start its growth cycle. Then the cell is inserted into a segregate and the cell develops normally.
 * Applied:** Animal cloning provides the obvious benefit in that it allows scientists to create another organism without using the normal system of reproduction.
 * Synthesized:** The process of cloning is similar to the process of making copies. It creates a direct replica.
 * Advocated:** The moral and ethical justification for animal cloning is uncertain which is why many nations have a ban on all cloning processes. Additionally, it is clear that the process of human cloning oversteps a clear ethical line and risks fundamental human rights violations (of both the parent and the clone). However, the process of cloning provides multiple benefits such as repopulating lost species.

Sources: General Information: http://www.buzzle.com/articles/animal-cloning/ Picture: http://www.theintellectualdevotional.com/blog/wp-content/uploads/2011/01/dolly-fig-13-13.jpg

=[|Plant Cloning]=

=== **Described:** The root cells of plants are identical to the plant. They have the exact same DNA as the rest of the plant. If you take the root cell and culture it, you can very easily clone a plant. ===

eventually forming a new plant.
=== **Applied:** Plant cloning is used very often in agriculture. It can be used for a couple different things. For some plant cloning is very common. Some plants don’t need the help of scientists, they simply clone themselves. However in some cases cloning is used to reproduce a plant that has valuable characteristics. These would be the plants that scientist try to clone. ===

**Advocated:** Plants cloning is a very It doesn’t require a lot of work. Some reproduce by cloning. Cloning plants does no harm to them and it can be very helpful in agriculture.
Sources ** : ** [|http://science.howstuffworks.com/environmental/life/genetic/cloning1.htm__]

** Pictures: http://www.scq.ubc.ca/wp-content/uploads/2006/08/transgeniccrop.gif **
= = =[|Transgenic Animals]=
 * Described:** The process of genetic modification in animals is to isolate a specific gene of interest and to then insert that gene into a particular animal in order to give that animal a particular trait.
 * Analyzed:** This process is performed by inserting the desired gene (such as a gene that would make a cow immune to Mad Cow Disease) into the animal's genome. This insertion gives the organism recombinant DNA and that particular trait.
 * Applied:** This process is used to enhance animals. By inserting particular beneficial genes scientists can create hybrid animals that have multiple ideal functions.
 * Synthesized:** This process is similar to taking a car and then replacing certain aspects of the car such as the exhaust system or the transmission in order to create a more optimal vehicle.
 * Advocated:** Genetically modifying organisms is questionable. Economically, it can increase the products of animals; however, socially and ethically it poises unknown environmental risks and violates a natural organisms' intrinsic value.
 * Sources:**
 * General Information:** http://www.learner.org/courses/biology/archive/animations/hires/a_gmo3_h.html, http://www.ornl.gov/sci/techresources/Human_Genome/elsi/gmfood.shtml
 * Picture:** http://static.guim.co.uk/sys-images/Observer/Pix/pictures/2010/8/5/1281024360284/genetic-modified-piglets--006.jpg

=[|Transgenic Plants]=
 * Described:** The process of genetic modification in plants is similar to the process of genetic modification in animals. A specific gene is isolated and then inserted into a particular plant in order to give that plant certain characteristics.
 * Analyzed:** The process of genetic modification in plants is performed by inserting the desired gene (such as a gene that would increase the nutritional value of rice) into the plant's genome. This insertion gives the organism recombinant DNA and that particular characteristic.
 * Applied:** This process is used to enhance plants. By inserting particular beneficial genes, scientists can create hybrid plants that have desirable characteristics.
 * Synthesized:** The process of genetic modification is like the editing of a paper. Both processes involve the removal of certain things and the insertion of others in order to create an overall better final product.
 * Advocated:** As with the genetic modification of animals, genetically altering plants is questionable. The practice has certain benefits such as helping to address world hunger with increased yields, yet its use can lead to the creation and proliferation of destructive organisms like “super weeds.”
 * Sources:**
 * General Information:** http://www.learner.org/courses/biology/archive/animations/stills/as_gmo2.html**,** http://www.ornl.gov/sci/techresources/Human_Genome/elsi/gmfood.shtml
 * Picture:** http://news.bbc.co.uk/nol/shared/spl/hi/pop_ups/03/sci_nat_how_a_plant_is_genetically_modified/img/4.jpg

=__Gene Therapy Click on Animation Once There__=
 * Described:** Gene Therapy is a technique which scientists can use to correct defective genes responsible for disease development. There are 4 ways in which they can go about doing this. First and most commonly used is where a normal gene can be inserted into a location within the genome to replace a nonfunctional gene. Another way is an abnormal gene could be swapped for a normal one via homologous recombination. The abnormal gene could also be repaired through selective reverse mutation. The final way is to simply alter the regulation of a specific gene.


 * Analyzed:** Gene therapy works by correcting dysfunctional genes in a cell. It functions with the use of a virus to carry the new gene to the cell when inserted into the body. These are essentially the vectors of the process. Once it gets to the cell it functions just as any other virus would and inserts its DNA into the cell.


 * Applied:** Gene therapy can be used to repair problems within the DNA of cells that normally would lead to diseases. It has also been used to correct some disorders in certain cases as well. So it can be very beneficial to scientists and doctors looking to make patients better.


 * Synthesized:** The closest comparison I can come up with is viruses. Just like a virus takes over a cell and inserts its DNA in the cell, gene therapy technically just overrides the cellular DNA with some made in a lab. It seems to parallel very closely our chapter 19 studies.


 * Advocated:** Gene therapy is relatively new but has already had some ethical criticism on whether or not we should be fixing things like disorders. There also have been complaints on the expensive cost of the treatment. I would still argue that it is very beneficial because there are many other ways we have tried to cure diseases and disorders so it only makes sense that we accept one that has finally worked. At the point where it can only improve people's lives I have to advocate it. As far as the cost goes, with more time spent on it and the more it becomes a natural technique the cheaper the process will get.

media type="youtube" key="imL1Zmi3mWk" height="390" width="640"
Sources: http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml Video: Youtube.com

=[|Restriction Fragment length polymorphism] - go to Restriction Fragment Length Polymorphism=
 * Described:** Restriction fragments length polymorphism (RFLP) is the variations of homologous chromosomes. Restriction refers to the cutting of DNA by the restriction enzymes. Polymorphism is the variation of the homologous chromosomes.


 * Analyzed:** You can detect RFLP by using [[image:RFLPS.gif align="right"]] enzymes to fragment DNA. The restriction enzymes cut short sequences. The pieces are the separated by gel electrophoresis. RFLP has occurred if there is variation in the length of the detected fragment.


 * Applied:** Scientists use restriction fragment length polymorphism can be used to detect where on the chromosome a certain genetic disorder is located. In order to do this scientists would take a family with the disease and look for RFLP genes that have a similar pattern.


 * Synthesized:** RFLP’s are just like detectives. animations. help scientist figure out how to stop diseases just like a detective would solve a crime.


 * Advocated:** As scientist are figuring out how to stop genetic disorders, they need to know where the disease is in the cell. RFLP’s show them where the disease is on the chromosome. This makes it easier for scientists to narrow down what they are looking for and just focus on the certain point on the chromosome.


 * Sources: **http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/TechRFLP.shtml


 * Pictures: **http://www.google.com/imgres?imgurl=http://upload.wikimedia.org/wikipedia/en/thumb/b/bb/RFLP_genotyping.gif/360px-RFLP_genotyping.gif&imgrefurl=http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism&usg=__ESLvikIm168v4Q6uD7WXGCmOcj4=&h=206&w=360&sz=8&hl=en&start=0&sig2=NSMuPcZAiFgnZB8mqovT1w&zoom=1&tbnid=AEwh5Dow4mv48M:&tbnh=108&tbnw=189&ei=Q0RUTbLUIs_TgQerrOD4CA&prev=/images%3Fq%3Drestriction%2Bfragment%2Blength%2Bpolymorphism%26um%3D1%26hl%3Den%26safe%3Dactive%26client%3Dsafari%26sa%3DN%26rls%3Den%26biw%3D1223%26bih%3D574%26tbs%3Disch:1&um=1&itbs=1&iact=rc&dur=340&oei=Q0RUTbLUIs_TgQerrOD4CA&esq=1&page=1&ndsp=18&ved=1t:429,r:1,s:0&tx=113&ty=67

=__Genetic Profiles__ This is a method to get a genetic profile=
 * Described:** DNA profiling is a process in which scientists figure out distinguish the characteristics of your DNA. They will collect and analyze your DNA sample to create[[image:BXP0026100_P.jpg align="right"]] a profile of the unique allele sizes at several loci of your DNA. This profile is then called your genetic fingerprint.


 * Analyzed:** A DNA profile can be made many different ways. The way we used in class was gel electrophoresis. We compared the movement of the DNA fragments from each suspect and matched them to the DNA found at the crime scene. The most common way to collect DNA is the buccal swab.


 * Applied:** This process is very useful for many different things. The main use is in forensics and crimes. The discovery of genetic profiling led to huge advances in the ability to catch a criminal. In some cases it even exonerated people from jail because the DNA later proved them innocent. It has been essential in that field of work. Another way it could be used is to determine who the mother or father of a child is or simply just the relation of one person to another.


 * Synthesized:** All I can think of when I hear DNA profiling is television shows like CSI and all the others that put a huge emphasis on DNA evidence. While the real world of genetic profiling may not be a glamorous as hollywood makes it I still think it gives great insight into what goes into the process.


 * Advocated:** The method of using DNA profiling for crimes has been readily excepted by society because of the innumerable benefits it poses and just the fact that it can help to punish criminals. I am right along with them on completely agreeing in it's necessary use. However, there has been some controversy over taking a genetic profile of a baby when it is born and then keeping it on record. This mainly was only introduced in Britain, but I actually agree with that use of genetic profiling also. It is substantial in many areas and has the ability to find people guilty.

Sources: http://genome.wellcome.ac.uk/doc_WTD020970.html and http://www.dnajunction.com/tests/genetic-profiling.php Picture: http://marketplace.veer.com/images/BXP0026100