Taylor+Pytleski


 * Part 1 ~ DNA Cloning/Recombinant DNA/Genetic Engineering**

__Gene Cloning with Bacterial Plasmids__

 * DESCRIPTION:** Basically replication of DNA, but with recombinant DNA. (using plasmid and DNA of a chromosome). If cultured in vitro, vials and other materials are used.


 * ANALYZE:** You have a bacterium, containing bacterial chromosome and plasmid, and a cell containing the interested gene. the gene is then inserted into the plasmid (creating recombinant DNA). The plasmid is then reinserted into the bacterial cell. The host cell is grown in culture to from a clone of cells containg the "cloned" gene of interest. Gene cloning can be applied to various applications and research. (source: pg. 397 in textbook)

[|Gene Cloning Tutorial]


 * APPLY:** Used as disease models and gene therepy-efficient insertion of therapeutic genes at the appropriate chromosomal target sites within the human genome, without causing cell injury, cancer, or an immune response. Genes are also used for pest resistance in plants, alteration of bacteria, protein dissolves blood clots in heart attack therapy, or even treatment of stunted growth, and many more. (sources: textbook, and wikipedia)


 * SYNTHESIS:** Reminds me of normal DNA replication, or stem cell research, since there is a lot of arguementation on the usage of stem cells and the way of retreiving them in the scientific society at this point in time. Stem cells can also be used for multiple applications, just like the bacterial plasmid cloning.


 * ARGUE:** I think that gene cloning in bacterial plasmids is a useful application in biotechnology. It isn't harmful to our human society, like some of the stem cell extraction (since we have to extract those cells from our own body). This way, we can do basic research to discover many new and exciting solutions that could possibly help us and other organisms.



__ Nucleic Acid Hybridization __

 * DESCRIPTION:** To me, this process looks like a big saltine cracker inside of a plastic bag! The end product is like sheet of glass with a single dot displayed on it. :) (according to the figure in our textbook, i could not find an example online) Otherwise, looks like the process of transcription.




 * ANALYZE:** A technique in which single stranded nucleic acids, either RNA or DNA, interact to form hybrids. They are formed by molecules with similar, complementary strands (nucleic acid probe). If scientists know at least part of the nucleotide sequence of the gene of interest, they can synthesize a probe complementary to it. (sources: textbook and [|nucleic acid hybridization])


 * APPLY:** For the identification on the location of a clone carrying the interested gene. Scientist can also use the cloned gene as a probe to identify similar or identical genes in DNA from other sources. (source: textbook)


 * SYNTHESIS:** Reminds me of the transcription process, but with cloned DNA instead.


 * ARGUE:** Seems like a very long and enduring process. I think that it is very helpful to find the interested gene, but there is probably a faster, easier way of doing it somewhere :)

__Genomic Library__

 * DESCRIPTION:** Mini library containing plasmid clones. A collection of many bacterial or phage clones. Looks like many tiny crates filled with the bacterial clones. [|Video of Cloned Libraries]


 * ANALYZE:** A genomic library is a collection of many clones. Each clone carries copies of a particular DNA segment from a foreign genome, integrated into an appropriate DNA vector. In a complete genomic library, the foreign DNA segments cover the entire genome of an organism. (source: figure 20.5 in textbook)


 * APPLY:** Scientists today often obtain these libraries from another researcher, a commercial source, or a sequencing center.


 * SYNTHESIS**: It is basically a scientific library! Scientists can go in and use the cloned bacteria or phages to do research on them to help them out with their experiments.

[|Genomic Library Article for more information]
 * ARGUE:** I think the genomic library is a great idea because if we didn't keep and record what we already discovered, there would be a lot of time and energy wasted into doing the same procedures over and over again to seach for something that's already been found!

__Polymerase Chain Reaction (PCR)__

 * DESCRIPTION:** A quick method for cloning large quantities of a particular gene or DNA sequence. Copied many times inside a //test tube//. PCR is like photocopying one page rather than a whole book (gene analogy). (source: textbook)


 * ANALYZE**: The PCR procedure is a three-step cycle that rapidly amplifly DNA or a specific gene. 1. Denaturation: Heat briefly to separate DNA strands. 2. Annealing: Cool to allow primers to form hydrogen bonds with ends of target sequence. 3. Extension: DNA polymerase adds nucleotides to the 3' end of each primer. Basically, a heating and cooling process in able to replicate the specified. (source: figure 20.6 in textbook)


 * APPLY**: Used when the source of DNA is scarce and is used increasingly today to make enough of a specific DNA fragment and entirely skipping the steps of making and screening a library. PCR makes LARGE quantities of DNA in a short amount of time, and helps in the diagnosis of diseases ([|PCR]). I also learned from a previous class that PCR is used a lot in the forensic science field. For example, if they discover DNA at a crime scene and they need more of that DNA to run multiple tests, they use the PCR method to create more. :)


 * SYNTHESIZE:** Honestly, I don't think there is a faster or more efficient way to create large quantites of DNA. Polymerase Chain Reaction pretty much does it all for scientists. (in relation to replicating large amounts of DNA, that is). It's quick and easy and doesn't use a lot of complicated techniques.


 * ARGUE:** PCR is definitely a plus for me. Scientists, and even everyday people, can perform the PCR method. It helps solve crime and uncover new discoveries :)

**Part 2 ~ Studying Expression and Function of a Gene** __ Gel Electrophores is __ **DESCRIPTION**: A huge chunk of ice inside of a bath. :) The final result is like a piece of glass with fluorescent lines all over it. (DNA fragments!)
 * ANALYZE:** Gel electrophoresis is a technique that uses gel made of a polymer, and it acts as a molecular sieve to separate nucleic acids or proteins on the basis of size, electrical charge, and other physical properties. Since DNA is negatively charged, when inserted into the cathode (-) it automatically travels towards the positive pole. The longer fragments move much slower than the shorter fragments do, and therefore, in the result, you can distinguish between the different sizes of the nucleic acid molecules. :) (source: textbook) ([|Click HERE for a virtual lab!])


 * APPLY:** Used to provide genetic information such as criminal cases, diagnose genetic diseases, and to solve for paternal cases. In most cases, PCR is used in collaboration in order to have a surplus of DNA. Interesting fact! Proteins can also be run on gels. (source: [|Gele electrophoresis])


 * SYNTHESIZE:** If I were a scientist, I would used the method gel electrophoresis in collaboration with PCR (as mentioned above) and also Southern blotting, which I go more in depth in the next few paragraphs. These few methods used together can be very helpful and aid in the solving of crime as well if DNA is discovered. :)


 * ARGUE:** I like the technique of gel electrophoresis. I've had the privilage of actually seeing this done, (fast version), and it is pretty neat! It can help in many cases, like waht if you wanted to find you your birth father? You wound take your DNA and his DNA and compare if you both have any matching bars. Voila!

__ Southern Blotting __

 * DESCRIPTION:** Blotting, when you hear that word you think of spots right? Wrong. It really is just a technique that combines gel electrophoresis and nucleic acid hybridizations to help identify carriers of mutant alleles. Southern is the name of the biochemist Edwin Southern who came up with this technique.
 * ANALYZE:** Southern blotting is a 5 step procedure. 1) Preparation of restriction fragments. 2) Gel electrophoresis (see above) 3) DNA transfer (blotting). 4) Hybridization with radioactive probe. 5) Probe detection. (source: textbook) ([|Great animation on Southern Blotting!])
 * APPLY**: Southern blotting is applied with gel electrophoresis and nucleic acid hybridization to help detect the heterozygous carriers of a certain gene, along with a few others like gene mapping and detection of diseases. It has been a laboratory workhorse for many years. (source: textbook)


 * SYNTHESIZE**: Using this method in collaboration with PCR amplification to identify more specific parts of genomes. This technique is a spin-off from gel electrophoresis. (Notice that PCR is used a lot in biotechnology!!)


 * ARGUE**: Southern Blotting seems like a lot of work, but helps in the long run. I would probably try and find another way around it if I could, since you have to do basically 3 different methods to find out a certain one thing. (gel electrophoresis, nucleic acid hybridization, and then the blotting)

__ Microarrays __

 * DESCRIPTION:** It's stop-and-go lights gathered together on a black background! Well, that's what I think at least. Really, it's a collection of microscopic DNA spots attached to a solid surface.The microarray is also called the DNA chip, since it sort of looks like a computer chip. These fragments represent all the genes on an organism. (source: textbook)


 * ANALYZE:** The technique occurs in four steps: 1) Isolate mRNA. 2) Make cDNA by reverse transcription, using fluorescently labeled nucleotides. 3) Apply the cDNA mixture to a microarray. The cDNA hybridizes with any complementary DNA on the microarray. 4) Rinse off excess cDNA; scan microarray for fluorescence. Each fluorescent spot represents a gene expressed in the tissue sample. (source: textbook) (see below image)
 * APPLY:** DNA microarray assay can test thousands of genes simultaneously to determine which ones are expressed in a particular tissue, under different environmental conditions, in various disease states, or at different developmental stages. They can also look for coordinated gene expression. (source: figure 20.15, textbook)


 * SYNTHESIZE:** This method sort of reminds me of nucleic acid hybridization in a way. In that technique, the single-stranded probe can base-pair with any complementary DNA on the membrane, whereas in the microarray assay, the cDNA //hybridizes// with a complementary DNA. (far-fetched, I know) :)

[|VIRTUAL TOUR]
 * ARGUE:** I like this method because scientists can test //thousands// of genes at the same time to test for a particular gene, instead of doing it one. gene. at. a. time. Also, I think the DNA microarray's end result. It is pretty :)

**Part 3 ~ Cloning Organisms** __ Plant Cloning __ **DESCRIPTION:** We all know how cloning works: the offspring looks EXACTLY like the parent! So for a plant, let's say a daffodil, the offspring looks, well, like the parent daffodil!
 * ANALYZE:** First of all, you have to cut off a piece of the root of the designated plant you want to clone. Then you culture the fragments in a nutrient-medium and stir, which causes the single cells to shear off into the liquid. Single cells free in suspension and begin to divide. Embryonic plant is developed from a cultured single cell, and the resulting plantlet is cultured on agar medium and later planted in soil. Voila! (source: textbook) [|Click here for more details on Plant Cloning]


 * APPLY:** Plant cloning is used extensively in argriculture, and some plants actually reproduce themselves from cloning, like orchids. (source: [|Plant Cloning Uses])
 * SYNTHESIZE:** Plant cloning...what do I think of when that is mentioned? Exactly how it's said. Cloning. It's just amazing how you can get an exact duplicate from experiments and methods!


 * ARGUE:** I think any type of cloning is neat. Although, I think that every little thing should have it's own significance in this world. So cloning goes against my morals, so to speak. BUT, argriculture uses cloning a lot, and even though I'm not big into farming, they're research and experiments can help our world one little step at a time. :)

__ Animal Cloning __

 * DESCRIPTION:** Cloning is cloning, and animal cloning is no different. Just like plants, animals can be cloned, Dolly being the first cloned mammal-a sheep. The description is the same as the plant cloning, you have a parent egg, and the offspring will result in an exact copy!


 * APPLY:** The cloning of an animal occurs in 6 steps as follows: 1) Cultured mammary cells are semistarved, arresting the cell cycle and causing dedifferentiation. (cells are obtained from a mammary cell donor). 2) Nucleus of an egg cell of an ovary is removed (this egg cell is from another donor, just the cell will be used, no nucleus) 3) The two cells are fused. 4) The resulting cell is grown in culture. 5)The now early embryo is implanted in uterus of a third donor. 6) Embyronic development soon follows. (source: figure 20.18 in textbook)
 * APPLY:** Some scientists use animal cloning for livestock breeding, to make a desired cow or pig with the certain traits that they want. (source: [|Animal Cloning Uses]) Others hope to use animal cloning in the future for medical purposes (animal models disease and for stem cell research), reviving endangered or extinct species, and possibly clone humans (infertility, or deceased child). (source: [|Addtional Animal Cloning Uses])


 * SYNTHESIZE:** I would also use cloning in general for research. Obviously I would like to use animal cloning for medical purposes mainly, since I want to become a doctor someday,the medicine part interests me. Saving lives is what I want to be a part of, and animal cloning could possibly be factor in helping to find that.


 * ARGUE:** Like I said, cloning is pretty neat and it's amazing how far science and technology has gotten us today. But, last year we took a class trip to Hematech laboratory in Sioux Falls, which is a place that tries to clone cows for argriculture benefits. Like I've said before, I think that getting an actual duplicate is amazing; I would hate to be the cow that is put under that kind of pressure all the time though.They poke and prod and inject needles into all the cows just to run research and extract eggs and blood. I couldn't watch, and I felt very sorry for the animals. I love animals, and if they found a better way to not run research like this, I would approve of animal cloning more. Also, I think that animals should have a different personality to each. No one animal is alike, which cloning contradicts that.

**Part 4 ~ Practical Application of DNA Technology** __ **Restriction Fragment Lengh Polymorphism (RFLPs)** __ **DESCRIPTION:** RFLP is basically another version of gel electrophoresis (the resulting appearence that is). There are markers and with those, scientists, and us, can determine multiple things. We'll get more into that later :)
 * ANALYZE:** The technique for RFLP starts with fragmenting a piece of DNA by restriction enzymes. Those fragments are then separated by gel electrophoresis and then transferred to a membrane by the Southern blot procedure. Hybridization then takes place to a labeled DNA probe which determines the lenghts. Each fragment length is considered an allele. (source: [|Click here for more infromation])


 * APPLY:** RFLP was the first DNA profiling technique inexpensive enough to see widespread application. RFLP analysis is used for genetic fingerprinting, genome mapping, localization of genes for genetic disorders, determining risk of disease, and especially paternity testing. (source: wikipedia)


 * SYNTHESIZE:** This technique is used in collaboration with gel electrophoresis, Southern blotting, and hybridization. (see above) See what science can do for us when we combine methods?!? It is really fascinating.


 * ARGUE:** This method is very hand for scientists because it is one of the inexpensive techniques to perform. I like this method because you find a variety of different information from it, but you have to do many different appliactions to get to it, so it is probably time consuming. All in all, I am all for this :)

__ Gene Therapy __

 * DESCRIPTION:** Gene therapy introdroduces genes into an afflicted individual for therapeutic purposes. They remove the designated allele from one source and insert it into the cell that is defective, so to speak. Think of the word "therapy", scientists are trying to //help// the somatic cell that is in need!
 * ANALYZE:** Some gene therapy uses a retroviral vector to help the certain cause. This occurs in 4 steps: 1) Insert RNA version of normal allele into retrovirus. 2) Let retrovirus infect bone marrow cells that have been removed from patient and cultured. 3) Viral DNA carrying the normal allele inserts into chromosome. 4) Inject engineered cells into patient. If all goes as planned, the patient will get healthier and the cells wil begin producing the missing protein. (source: figure 20.22 textbook)
 * APPLY:** Gene therapy is obviously used for therapeutic purposes, and it also holds great potential for treating disorders traceable to a single defective gene. Many diseases are the result of just one gene, like sickle cell anemia, cystic fibrosis, and SCID for example. With this method, we can help save people's lives. (source: [|Uses])

[|Newspaper Articles]
 * SYNTHESIZE:** This technique needs to have cloning involved to clone the designated gene. A retrovirus also takes place, so reverse transcription occurs as well. If I had one of the diseases that occurs from one gene, I would consider this method. Most patients heal well from it, and only a few have obtained cancer from it. But with our new and improving technology daily, gene therapy will be the least of our problem. :)


 * ARGUE:** I absolutely love this method! Like I've stated earlier, I want to become a doctor someday and this is something that could truely make a difference for people with single gene related diseases. It's amazing how one gene can cause huge problems if missing or defective, and gene therapy is help prevent this or fix the problem :) :)

__Transgenic Animals__ DESCRIPTION: A transgenic animal is an animal that carries a gene from another source that has been deliberately inserted into its genome. Really, the animals look the same as they mostly do, just they produce a completely different object than their own...( like proteins for example). :)

ANALYZE: Creating a transgenic animal results in producing recombinant DNA, some DNA from the animal being used and some from the designated organism that scientists want the product to be made from. They then insert that DNA into the host, and the host soon creates the subject that they want. For example, let's say you wanted to create a large amount of protein products, you gather a host (goat) and then insert recombinant DNA that you already created into the goat. Later, you can obtain the protein that it secreted through the goat's milk! AMAZING! (source: textbook)

APPLY: Transgenic animals are mainly used for pharmaceutical purposes. They are sometimes considered "pharm" animals because they house the proteins that are being created. They are also used as disease models. Transgenic animals are just another way of producing large quantities of protein products instead of doing it //in vitro//, in a lab. (source: textbook) [|TOP 10 TRANSGENIC ANIMALS!]

SYNTHESIZE: Like I stated earlier, the use of transgenic animals is combined with recombinant DNA transformation. If I could change one thing about this method, it would be to not put animals through all this research. Maybe give them a break sometimes.

ARGUE: I think it is neat that you can make a kitten fluorescent, or an elephant turn pink, but if you were the animal would you like to be put through that? Maybe, if you had a say in it. But animals do not. There is nothing I can say to change that, but going through animals is probably the safer way to go than //in vitro//.

__Transgenic Plants__

**DESCRIPTION:** The description of transgenic plants is the same as animals. They all look the same, UNLESS you input a gene that alters the appearence (see below picture).
 * ANALYZE:** The procedure for creating transgenic plants is basically the same as creating transgenic animals. You have to first create recombinant DNA, or in this case plasmids, and then insert that into the designated host plant.


 * APPLY:** There are a few more uses for transgenic plants than there are for animals, here are a few: improved nutritional quality, insect and disease resistance, herbicide resistance, salt tolerance, "terminator" genes, and biopharmaceuticals to name a few. (source: [|Transgenic Plant Uses]) In 2007, the FDA approved a plan to plant over 3,000 acres in Kansas with rice harboring genes for milk proteins. The harvested proteins would be used in rehydration formulas to treat infant diarrhea. Since the beginning of time, natural plants have been used to help heal us from diseases, so why not alter them to be for efficient?! (source: textbook)

[|Transgenic Plant Articles]
 * SYNTHESIZE:** Transgenic plants remind me of gene cloning (first section of this project). In gene cloning, a recombinant DNA is produced, with the host DNA and a plasmid. Same goes for transgenic plants! I like the idea that animals are not put under all the pressure as well :)


 * ARGUE:** I love learning about plants and especially the different types of uses that can be come up with by using plants to help us! I am all aboard this method. :)

__Genetic Profiling (DNA Forensic Testing)__ **DESCRIPTION:** A person's genetic profile is basically a person, but their DNA! Each person is unique, and therefore their genetic profile is as well. It is referred to as a "DNA Fingerprint" by forensic scientists. It shows a person's DNA sequence.

**ANALYZE:** To identify a person accused of a crime, forensic scientists look at STRs, or short tandem repeats. These are tandemly repeated units of 2- to 5- base sequences in specific regions of the genome. In EVERY person, these repeats are highly variable, and therefore are unique, making a person's genetic profile unique, and hopefully bringing the criminal to justice. Although, The Innocence Project - a nonprofit organization dedicated to overturning wrongful convictions - uses STR analysis of archived samples from crime scenes to revist old cases, and 18 innocent people have been released from prison as a result of forensic and legal work by this group. (source: textbook) [|Video of the Innocent Project]

**APPLY:** All in all, genetic profiling is used to identify individuals. It is very useful to forensic scientists in ruling out a criminal, but also can be used for paternity testing and identifying personals in mass casualties. Forensic scientists used genetic profiling after the World Trade Center attack and identified almost 3,000 victims! (source: textbook)

**SYNTHESIZE:** This method is combined with PCR, to multiply DNA, and also electrophoresis, to determine the lengths of the DNA. Southern blotting is not required, but is quicker than RFLP analysis. Basically, all of the techniques we've learned thus far is gathered and recorded into an individual's genetic profile. AMAZING! (source: textbook)

**ARGUE:** Genetic profiling is fun! I love forensics with a passion, and discovering criminals or the identity of a loved one would be a fantastic job to get a hold of. Without genetic profiling, the identification of people (without them actually being there) would be immensely difficult.