Abi

Hi I'm Abishek Padwal and I am from San Jose, California. I recently got more interested in biology after taking Honors Bio at my school, Archbishop Mitty, and I took this opportunity to get ahead in biology for college. I have a large family of six and a dog, Bentley, who is smart, yet mischevious. At my high school I am part of the Junior Varsity Swim Team, and am also in Chess Club. Recently, however, I have signed up for math team and my school's new biology club. My favorite book has to be the Power of One by Byrce Courtenay, and my favorite movie would have to be Rambo (The First Three Installments).

My Project Is Included Below:

__HIV RECALL CELL:__

//Basis of the Recall Cell://

It is not surprising why scientists have not found a permanent cure for HIV. The truth of the matter is that most scientists today want to find the invasive positions in the virus, like a receptor or a gene, and try to tamper with it in the hopes of finding a cure. This harsh method, however, will always be futile as the HIV cell will always evolve if it feels evolutionary pressures threatening its way of living. This is simple evolutionary principles that are always in action and should really be taken into account by people. Going out of this thinking, the Recall Cell is a new vaccine to counter HIV in a way that will not let it evolve, but will also make sure that it fulfills the promise of keeping the immune system safe. The way that we plan to approach this method is by giving the HIV virus something better than the CD4+ cells, the Recall Cell. These cells will have a large number of “bonuses” that will allow for the HIV to become “Evolutionarily Attracted” to the cells, or in a way they will be forced by evolutionary purposes to take the Recall Cell as their host for its better benefits. This will give a respite to the CD4+ cells that have been the punching bag for the virus ever since its transfer from animals to humans. These benefits that we give the virus are mainly focused around helping it replicate, contrary to the invasive attack measures that are usually perpetrated against it. This factor will be substantial to the medical field, as there will be only one time where they have to focus on the subject, and therefore more time finding out other things and try to solve other problems.

//Structure Basis://

This Cell will be Eukaryotic, with no actual connection to any immune system cell besides having CD4 on the outside. The main two functions that it will perform with the HIV virus will be to speed up the transcription and protein synthesis time. Any run of the mill cell will work as the proxy, and we will only need one that we can grow in culture. After we harvest that cells descendants we can keep the culture forming and propagating as separate entities, and we will have a continual supply of these cells. When somebody needs to make another batch, they can just reread the instructions. We have about half and half of our genes being synthetic or modified combinations of other genes. __GENES FOR MAKING EVOLUTIONARY BONUSES DISSCUSSED ABOVE__:

//Genes Out of These That You Need To Look At For Modification To Allow ATP Synthase to Be Used w/ viruses// Synthetic Gene Specifications: CD4 Hook for Initial Viral Capture. Would need to be a sequence in which the hydrogen bonds (secondary stage) cause the folding and nothing happens to the other molecules. It would have to be comprised of CD4, and have to be able to exert its positive charge on the negative ATP synthase, or possibly just make a specific connection between synthase and CD4, like by adding a glycoprotein to the side of ATP synthase you are making.
 * ATP5G1 ATP5G2 ATP5G3 (control f0 complex)**
 * Synthetic Gene **

(need to modify so that you take the whole atp synthase and put it in the microtubules and in the membrane of the cell, also need to modify the ATP synthase with these three genes above so that the ATP synthase works off of the passing of the HIV virus into and out of the cells, which would mean you would have the surface molecules usually involved in the membrane entry of HIV, CD4 and gp 120, be the two molecules that have to connect to allow the ATP synthase to start working, the CD4 will replace the Aspartate on the motor, and it will protrude far from the actual cell membrane so that it is the first thing to come in contact with the virus, and not the other regular phospholipids of the cell membrane, this will allow the virus to choose the point of entry and come through the ATP Synthase Tunnel.)

(might also want to have people with HIV suggest cremation after passing away as to insure that those Rekall Cells do not escape into the environment, as they might share their genes with other cells and have the mitochondrion become ineffective) One other factor will be protection of these pathways. Since the gateways will actually be the ATP Synthase molecules, we just need to have a way to selectively have HIV be the one that can access the ATP Synthase. This can be achieved by using the genes above, which will alter the ATP synthase so that However, there is the possibility that we could scrap this whole method and let every type of bacteria and virus come in, as if they use the cell to replicate, this could be a perfect solution for them and the Rekall Cell could become a universal cure for all diseases that replicate inside cells.

//Genes for Making the ATP Synthase Big Enough For The HIV// ** 5x Building Block Protein Sequences in DNA **

We need to account for the new size we make with these ATP synthases that will be modified to take in HIV. HIV is exponentially bigger than a single Hydrogen Ion, so the ATP synthase has to be huge. This can be easily achieved by divulging down into the most basic parts of the ATP synthase structure, the protein building blocks. These blocks can be multiplied by putting their genes down multiple times in the place where only one would be, and doing this for all of the genes in question. In this case that would mean all of the genes in the next section. It might take up more of the cell membrane space, but that is okay as we want to try and draw the HIV into the cell through these points, so it is almost now like forcing them.

//Genes for Putting The ATP Synthase Out on the Phospholipid Membrane and in microtubules// ** Incorperate ATP5D, ATP5E, ATP5F1, ATP5G1, ATP5G2, ATP5G3, ATP5H, ATP5HP1, ATP5I, ATP5J, ATP5J2, ATP5S ATP6, ATP6AP1, ATP6AP2 ATPSBL1, ATPSBL2 MT-ATP6, MT-ATP8, ATP5A1, ATP5AL1 ATP5B, ATP5BL1 ATP5C2, ATP5L, ATP5L2, ATP5O (ATP5G1-G3 with past modifications) all modified to have signal molecule (a gene on their person that allows them to direct motor proteins, changed to be guided to the membrane, when there they will naturally form in the membrane) ** We need to have the phospholipid membrane contain the parts to the ATP synthase. In order to do this gene transfer we will need to put the genes above into the cellular membrane genes. We would have to put these genes in question into the middle of the DNA as this is where it is in the mitochondrial membrane DNA and therefore is the probable place where the DNA for the synthase will proliferate to put ATP synthase molecules all along the membrane. In order to allow an exit route, we will need to have the same system in the reverse direction of the others. In other words, we will need the recall cells to be able to handle the viruses coming out. For this we would need the DNA template for ATP synthase to have its gene order reversed, and then its genes will be implanted in the middle of the genes for microtubules and membranes as well. //Genes Needed Modified For Making Microtubule Transport Faster://
 * DYNC1H1, DYNC2H1 **

These Genes that code for motors should be modified so that they run faster across the cell, whether that means that they receive more ATP or they attach better. Try to find something that would allow the cells to run these faster. Though make sure that you do not run them too fast, as that would not allow the HIV cells to make DNA copies of their RNA, which they do in microtubules while on the move to the nucleus. There is also the possibility that we can modify how they connect to the actual microtubule to try and make the ride smoother or require less energy to manage, so we can focus totally on speed with the residual ATP. One way to make the ATP worth more would be making the RNA polymerase a little lighter, so that the energy to size ratio is maximized and one phosphate group from one ATP can do a lot more work. //Genes Needed For Making NFKB Transcription Factor Present in The Cell://
 * NFKB1, NFKB2 **


 * Over stimulant: Any Strong Promoter **

These Genes need to be modified with a strong promoter that will run the process of transcription all the time. This method will allow the cell to openly express these genes all the time. This will allow another bonus towards HIV as it needs NFKB to run its replication process. So in reality it will have the “go signal” to produce its own parts already present, and therefore will be able to replicate much faster. //Genes Needed To Add Twice The Ribosomes//


 * 2x All RP and RPL Genes **

You would need to modify these genes in order to allow for the construction of twice the ribosomes, and this would be enticing for the HIV cells as it would be able to have twice the amount of its viruses in the cell at all times, as they have twice the construction materials that they can use to make themselves. This would require expressing the gene twice on the same template. //Genes Needed To Make an Effective Immunity of Recall Cells for Periods of Time//
 * HLA B w/ Any Cleaved Part From HBA or HBB Gene Series and w/ HBA and HBB containing a different signal sequence that attracts to the membrane. **

These genes control what molecules are presented to the CD8 t cells when they do their inspections of cells. The HLA B actually codes the MHC molecule, and the HBA and HBB gens are what it presents. To modify this you need to be able to find a way to permanently place “Doolittle Brooms” or fake pieces of proteins in the MHC molecules that distort the protein count in the T Cell Receptor as it is reading the numbers. This will be in this case hemoglobin. Usually the pieces of proteins from HIV or a cell with HIV would be present, and this would allow the cell to be used as a “speak easy” for the HIV cell, where it can relax knowing it can freely replicate. These HBB and HBA brooms need to get into MHC by having their signal coding changed so that they direct towards the membrane instead specifically the MHC. Once there the vesicle should be degraded, and the There is some risk, but it is minimized by using the Eukaryotic Cell Process. This could be also considered as a benefit, as the HIV has a stable source of replication and will stray away from the uncertain CD4+ cells. You might need to allow HIV to take over some of these in order to be able to express its genes, but in this case you should make the MHC with the Doolittle Brooms look more enticing, or have them stand out versus the other parts of the cell. To do this you could //Genes that are “Dead Genes” That Will Be Used as extra sites for HIV DNA to attach to//
 * Synthetic Gene **

Specifications: Small, only about three codons long, with only the promoter region and the small ORF being the only things present. These small “dead genes” will code for useless molecules, therefore allowing for the cell to continue on with its processes without worrying that these molecules will cause any obstructions. These places however will allow the HIV DNA to have more places to bind in the cell. More places to bind, coupled with bigger Nuclear Space, allows for more HIV viruses to be encoded inside the cells. Since HIV has to choose between one or the other (CD4+ cells or Recall Cells) they will choose recall cells as they are easier to use and more beneficiary. Given that many synthesized genes are longer than 3 codons, it will be pretty easy for a laboratory to make this gene, which will only have to be put in the first “culture” of these cells in order for it to be able to spread. //Genes Needed To Give ATP to the HIV cell// ** Synthetic Gene ** Specifications: This Gene will encode a protein that has a favorable (easy) ability to bond to the phosphate groups on ATP (possibly through the use of two carbons needing bonds on the synthetic structure). This gene will contain a signal sequence that will allow the ATP to be vesicle transported to the Ribosome for the cellular membrane ATP synthases, and to the nucleus for ATP made from ATP synthase in the microtubules. The gene will also have its own signal sequence that migrates it to the membrane in the first place, and possibly an operon like machine could be used where the second signal sequence is turned on by the contact of ATP. This act of giving extra ATP to the cell is important as it will give HIV its own set of materials for making its cell, and therefore it will proliferate more and become more populous in the recall cell. The HIV virus will therefore deduce and evolutionarily positive outlook on the Recall Cell, and possibly use it more in the cell. We also might still be able to keep the bonus that HIV is bound to the Recall Cell if we instill that unless they use our cell, they will not get extra ATP.

//Genes Needed To Make Double The Golgi Apparatus// ** 2x Golgi Gene ** If we make twice the golgi bodies, we will be able to allow HIV the “fast pass” to get cetain things modified in the golgi apparatus. Whether we like to think about it or not, the HIV virus probably has to wait some time to get its materials through the Golgi Process, as the cell still carries on with its functions while the virus does its business. This little change in timing will be a part of making the viral replication process faster, which will be evolutionarily appealing to the HIV virus, and it will want to use this cell more. //Genes That Encode Faster, HIV specific RNA Polymerases//
 * Speed Modifications #1: POLR2I and POLR2A (physically attach nucleotides) **


 * Speed Modifications #2: POLR2G, POLR2F, and one unknown (could be like sigma factor) **


 * Balance Modfications: POLR2G, POLR2F, and one unknown (stabilize molecules) **


 * Promoter Modifications: Medium Promoter **

These Genes Code for a DNA polymerase that need to be modified to work faster. We achieve this through trying to add more atp to the equation (like with the atp gene) or letting the molecules pass some of their “checkpoints in copying things”. We will have these features in special RNA polymerase molecules that will also contain a modified run plate similar to the sigma factor. With this technology we will be able to code for the HIV parts much faster than the CD4+ cells and therefore produce more viruses. This will be evolutionarily favorable for the HIV and it will migrate towards using this cell for those purposes. Therefore the CD4+ cells will not be prayed on by the HIV virus and they can function to rebuild the immune system. We need to see and increase to about 3 nucelotides a second from less than 1/10 of that number. The first set of molecules could be modified to put the nucleotides in faster, and the second pairs could be modified to run smoother along the actual DNA. The Balance Modifications will allow the polymerase to try and stabilize itself with a faster run time on the DNA (so it does not fall off). The Promoter Modifications will allow for the cell //Genes That Regulate Density Dependent Inhibition//
 * Synthetic Gene **

Specification: We would need to include the Bonnie Bassler quorum system in the cell. In other words we would have to make a gene that codes for receptors that will appear on the surface of the cell and therefore they will communicate. However, when this quorum sensing goes, they will all slow down their replication by inactivating one of their protein genes for a period of 24 hours. This gene codes for a gene that regulates density dependent inhibition, and tunes it to be even more stringent in the host cells. This stricter measure of Density Dependence will allow the cells to still populate, but not exceed the number where they become a disruptant force in the body. This is still a problem for us in these cells as there is the high probability that all the new ATP and bio-products being generated in the cell as a method of combatting HIV infection in CD4 cells will likely However, another form of negative density dependence is the own molecules themselves. There is the slight possibility that when the cells multiply, and when HIV does not, there could be the possibility that there are too many Recall Cells for too little amounts of HIV. HIV does not take a quick reproduction route like bacteria, and even with these speeded up processes there is still the possibility that this will happen. If this situation occurs, the Recall Cells are basically out in the open as they need constant entry of the HIV virus to generate their ATP, so they would die as they would be lacking ATP from not enough viruses coming in. The main way that we aim to control cell growth, however, is having the cells extra genes that encode for ribosomes and more golgi slow down the cells growth as they will take up ATP that could have been used for growth. //Genes Needed For The Repairing Molecules To Use Viral Membrane To Repair Lyses// ** Synthetic Gene ** Specification: This gene will code a protein that will latch on to the negative charged oxygen with positive carbon molecules. The genes will comprise of the same system as in the bringing ATP to the ribosome and nucleus and will constitute one signal sequence making the protein go to the outside of the membrane to collect the phospholipids, and then the second signal sequence gene that will scatter the proteins around while attached to the membrane wall. The gene also has to have an array of glycoproteases that will cut the gp 120 molecules and gp 41 molecules off of the membrane. Then when there is a gap one of the molecules will eventually run up against it and will repair it with the phospholipid membrane. We needed this as a backup plan in case the cell does not work, but it will also be regularly to counter the effects of genetic drift. With genetic drift we see the fact that there will be some chance mutations in the HIV virus that will make some Viruses impervious to the method and they will continue on their original replication path. This will mean that the viruses will lyse the cell, and this is the factor we are trying to counter with this gene change. This gene encodes an enzyme that will be suspended in and around the cell. When the virus releases its phospholipid membrane, which is really from a human cell, the enzymes will take ahold of this and then take the materials to the membrane, when or if there is a lyse the enzyme will go over there (timing will be mitigated by a sensor) and put the phospholipid membrane in. Most likely the charges on the actual bilayer part will align themselves, and we have an efficient repair of the cells. //Genes That Make Twice the Amounts of Nuclear Membrane// ** 2x Actual building block molecule genes ** These genes will serve the purpose of when being translated, giving twice the amount of building block molecules as before, so the code can basically stay the same with the membrane growing to twice its original size. //Genes That Calm Nearby Cells Next to the Recall Cells//
 * Synthetic Genes (Offensive and Defensive) **


 * Negative Stimulatory For Immune System: IL10 or TGFBR3 genes w/ a modification where they only have their affects last for about 15 seconds. (Incorporate into the signal transduction pathway as the effect, with a stimulus molecule in the cell) **

Specifications: We will be using a system here similar to what Bonnie Bassler pioneered with her research group at Princeton. Receiving Gene and Offensive Gene need to be present, Receiving Gene needs to be an array of sensors secreted around the cell that can sense for the gene ENV. When this ENV gene is encountered they should send signal molecules out (something they also need to be coded for). The release of signal molecules should power a signal transduction pathway that will in turn release a call for other recall cells. This should make them come over and try to attach to the ENV arms. There should be a gene to code for this kind of behavior, and there should also be a gene part in there that codes for partial aggressiveness, so they do want the ENV gene and will push other cells out of the way to get them. The offensive gene will have to code for a vesicle that spans membranes that will allow for this kind of transfer to the other cell. This gene encodes for a receptor that will be secreted from the Extra Cellular Matrix and will stay in the area around a cell. When the ENV genes in HIV tries to attach to the other cells by using the Recall Cell as a proxy, the sensors will relay the signal back to the recall cell, and it will signal other recall cells to try and cluster around that triggered receptor, and try to make that connection between their CD4 molecules and the ENV gene. This would stop an effect from a connective encounter between nearby cells and HIV, but also the presence of the triggered receptor will allow the Recall Cells to release a neuro-stimulatory factor that will calm the cells down, so that they know that they are being taken care of. This calming will also be supplemented with the fact that CD4 containing cells (the recall cells) will be present once again next to the nearby cells, and they will again feel “reassured” that they are not the only CD4+ cells in vicinity. __PowerPoint:__ Bibliography //Wikipedia.Org, Wikimedia Foundation, web// //Ncbi.nlm.nih.gov, National Library of Medicine, web// //Answers.yahoo.com/, YAHOO! Inc., web// //Www.genecards.org/, Weizmann Institute of Science, web// Www.news-medical.net/news/2009/04/22/48630.aspk Jvi.asm.org/content/78/9/4541.short Www.sciencedaily.com/releases/2011/02/11022092607.htm http://www.cs.stedwards.edu/chem/Chemistry/CHEM43/CHEM43/Glycoproteins/Glycoproteins.HTML http://www.webmd.com/vitamins-supplements/ingredientmono-827-RIBOSE.aspx?activeIngredientId=827&activeIngredientName=RIBOSE http://www.rcsb.org/pdb/101/motm.do?momID=72 http://www.bing.com/images/search?q=mhc+class+i&qs=AS&sk=IM2&FORM=QBIR&pq=mhc%20clas&sc=88&sp=3&qs=AS&sk=IM2#view=detail&id=2AAEF3EE2F031CB620A40BDCBF2F0084E775C7D8&selectedIndex=1 http://www.sciencedirect.com/science/article/pii/S1389172311001149 http://www.bing.com/images/search?q=hiv+lysis&FORM=HDRSC2#view=detail&id=871E0484F5CC8023A053C97704640C83944B1D0A&selectedIndex=8 http://www.bing.com/images/search?q=hiv+apoptosis+of+bystander+cells&FORM=HDRSC2#view=detail&id=D74E239E08621E56BE22D3F3D17783595B47067F&selectedIndex=1 http://www.bing.com/search?q=heterodimer&form=LENDF8&pc=MALN&src=IE-SearchBox http://www.cirm.ca.gov/about-stem-cells/creating-new-types-stem-cells http://www.uniprot.org/uniref/UniRef100_A8ACP3 http://www.russelllab.org/aas/charged.html http://www.uniprot.org/uniprot/C4ZZ15