Alu elements

Alu elements Introduction For centennials scientists and laymen alike have been awe-inspired and intrigued by the phenomena that is Alu elements. It is a family of short interspersed repeats that have mobilized throughout primate genomes by retrotransposition over the past 65 million years of primate evolution (Comas et al., 2001). Alu elements are regarded as Sort Interspersed Nuclear Elements (SINES) whose length spans 300bp. In close proximity to the centre of the Alu element itself, is a recognition site for the restriction enzyme Alu I, of which its name is ascertained. These Alu elements accounts for 5% of the human genome and is believed to have arisen from a gene that encodes the RNA component of the recognition molecule (Smith, 2005). Alu is a transposable DNA sequence that has the ability to repeatedly copy and insert itself into new chromosome loci i.e. jumping-genes. More specifically Alu is a retroposon it necessitates the retrovirus enzyme reverse transcriptase to produce an identical copy of itself that has the capacity to be mobile. This is achieved when the inserted Alu, by processes of RNA polymerases, is transcribed into mRNA. The newly formed mRNA is converted to a double stranded molecule. This is accomplished by the action of reverse transcriptase. In the end, at any new chromosomal locus at the site of a single or double stranded break, the DNA copy of Alu is integrated (Robinson, 2005). In order for an Alu element to self transcribe, each has an internal promoter for RNA polymerase III. Nevertheless, it lacks the ability to produce a copy of itself. Furthermore, to integrate this copy into a new chromosome position. But other transposons the very functions Alu lacks. One of these other transposons is L1, a Long Interspersed Nuclear Element (LINES), as a results of LINES ability to retain a functional reverse-transcriptase gene. In addition to LINES ability to reverse transcribe RNA to DNA , L1 reverse transcriptase is also able to produce single stranded nicks in DNA. If a chromosomal locus contains the sequence AATTT, the reverse transcriptase enzyme will produce a nick the polyadenalated tail of the Alu transcript hydrogen bonds to the TTT sequence at the nicked site. Thus creating a primer for for the reverse transcription. Enabling the DNA copy to migrate (Fisher, 2007). This representation depicts the efficiency of L1. Moreover, how L1 provieds the the fuctions for Alu tranposons. In essence, it shows how Alu is a parasite of L1 i.e. a remnant of an ancestoral retrovirus (Kass et al., 2007). This study examines PV92, a human-specific Alu insertion on chromosome 16 and which belong to the subfamily Alu Y. The PV92 genetic system has only two alleles indicating the presence (+) or absence (-) of the Alu transposable element on each of the paired chromosomes. It is aimed at extracting DNA, amplifying it and running it on a 2% agrose gel. The results attained will be analysed for the possible Alu insertion or deletion. It is hypothesised that with the aid of specific molecular biology techniques, analysis of the PV 92 Alu element can be achieved and the population will be in Hardy-Weinberg Equilibrium. Method And Materials A) DNA Samples For approximately 1minute, sterile nylon swabs were rubbed inside the cheek. The swabs were then placed in 250 µl of QuickExtract and rotated in such a manner that no solution was spilt. Thereafter, swabs were pressed against the sides of the tubes, removed the tubes were closed. The tubes were vortexed for 10seconds and incubated for 1minute at 65 °C. A second vortex then followed for 1seconds. The tubes were then incubated for 4minutes at 98 °C. Upon completion, the tubes were re-vortexed for 15seconds. With the use of a nanodrop, the DNA of each tube could be quantified. The expected yield for each tube was 20ng/ µl. B) PCR Conditions In a final volume of 150 µl, a standard master mix was prepared. Each master mix comprised 1x reaction buffer, 200mM dNTP mix, 1.5mM MgCl2, 1 µM of each primer and 0.016U/ µl of Taq polymerase. Following a 1:1 dilution, the DNA stock was diluted to a concentration of 15ng/ µl. The reaction was set up by mixing 15ng of DNA to a master mix which was made up to a final volume of 25 µl. Finally, the preparation of the negative control followed containing 24 µl of master mix which was made up to a final volume of 25 µl. The reactions were then run for 30 cycles by means of the subsequent constraints: 95 °C 1min, 55.5 °C 1min, 72 °C 1min and 72 °C 7min. This was then held at 4 °C. C) Gel Electrophoresis In an Erlenmeyer flask, 2g of agrose powder was weighed out and 100ml of 1x TBE was added. The agrose was dissolved by heating in a microwave oven. The solution was then cooled and 1 µl of EtBr was added. The agrose was then poured into a casting tray with a comb and this was allowed to set at room temperature. Of the PCR product, 10 µl was mixed with 1 µl loading dye. Then 10 µl of the newly formed sample was loaded onto the gel alongside the MW marker. Using a UV light, the DNA fragments could be visualised and photographed. The size of the amplified product could then be attained. Results Frequencies for a class of 70 students ++ = 35 individuals +- = 30 individuals = 5 individuals Therefore the total number of alleles = 140 Allele frequency distribution of the ++ and allele in the Normal Population Allele frequency for ++ allele = [(++ x 2) + (+-)] à · (n), where n= number of alleles in the whole population Therefore: Allele frequency for ++ allele = [(35 x 2) + 30] à · (140) =0.714 =71.4% Allele frequency for allele = [( x 2) + (+-)] à · (n), where n= number of alleles in the whole population Therefore: Allele frequency for L allele = [(5 x 2) + 30] à · (140) =0.286 =28.6% Observed Frequencies (OF) OF = Number of individuals for a specific allele à · total number of individuals in the sample Therefore: ++ allele = 35 à · 70 = 0.50 +- allele = 30 à · 70 = 0.43 allele = 5 à · 70 = 0.07 Hardy-Weinberg Equilibrium (HWE) The formula for determining HWE = p2+2pq+q2 Therefore: HWE = (0.714)2 + [2(0.714 + 0.286)] + (0.286)2 = 1 Comparison of observed frequencies with expected frequencies Observed Expected (O-E)2 à · E ++ 50 51 0.0196 +- 43 41 0.0976 7 8 0.1250 Total ∑ 0.242 For degrees of freedom = 1 and a 95% probability, the critical value attained from the Chi square table is 3.843 Discussion The results attained depicted that 35 individuals in the sample were homozygous for the insertion, while 30 were homozygous for no insertion. Only 5 individuals in the sample were heterozygous. This shows that a greater percentage of the population can pass on the PV92 insertion to their offspring. The allele distribution frequencies of the ++ and +- allele in the normal population revealed that 71.4% of the population was ++ which is just below 2 ½ times more that the 28.6% attained for the allele. The observed frequencies materialised similar results. The ++ allele had the highest frequency with +- having the lowest. Once more, the allele was the intermediate. When comparing the observed frequencies to that of the expected frequencies, the critical value attained was 0.242. With the respects to the Chi square table, for degrees of freedom being 1 and for a 95% probability, the critical value was 3.843. The Hardy-Weinberg principle implies that both allele and genotype frequencies in a population remain stable i.e. equilibrium, from cohort to the next except if specific disturbing influences are launched. Those comprise non-random mating, mutations, selection, limited population size, overlapping generations, random genetic drift and gene flow (Wikipedia, 2010 and Roux, 1974). With the above mentioned, it was attained that the sample was found to be in equilibrium as the calculated critical value was less than the one attained from the Chi square table at a 95% probability. Therefore, it can be said with much certainty that the hypothesis made was true. References * Comas, D., Plaza, S., Calafell, F., Sanjantila, A. and Bertranpetit, J. (2001). Recent Insertion of an Alu Element Within a Polymorphic Human-Specific Alu Insertion European Journal of Pharmacology Molecular Pharmacology Section, 247, 239-248 * Fisher, L. (2007). Alu Frame-set. (Online) (Cited 28 March 2010) Available from http://www.geneticorigins.org/pv92/aluframeset.htm * Kass, D., Jamison, N., Mayberry, M. and Tecle, E. (2007). Identificatin of a unique based Alu-polymorophism and its use in Human Population studies. Journal of Genes. * Robinson, N. (2005). PV92 Locus Alu: How to Track Human Migration Following This Gene Insertion. (Online) (Cited 28 March 2010) Available from http://www.associatedcontent.com/article/1452910/pv92_locus_alu_how_to_track_human_migration_pg2.html?cat=58 * Roux, C. (1974) Hardy-Weinberg Equilibria in random mating populations. Theoretical population biology. 5: 393- 416 * Smith, A. (2005). What is PV92? (Online) (Cited 28 March 2010) Available from http://www.fbr.org/swksweb/pv92.html * Wkipedia (2010). Hardy-Weinberg principle (Online) (Cited 28 March 2010) Available from http://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle

Factory Farming and Animal Cruelty Essay -- essays research papers

Factory Farming and Animal Cruelty Animal rights are practically non-existent in many different ways today. Factory farming is probably the worst thing they can do to the poor helpless animals. Factory farming effects chickens, cows, pigs, and many other animals that are used for food, milk and eggs. One of the biggest organizations against factory farming is called Compassion Over Killing (COK). They go to great lengths to protest and inform people about animal cruelty. Chickens have to endure suffering that no living thing should have to go through. The egg laying chickens have to be forced into tiny cages without enough room to stretch their wings. Up to 8 hens are crammed in to a cage that is the size of a folded newspaper, about 11"-14". Stress from the confinement leads to severe feather loss so the chicken will be almost completely bald in the cold cages. When the chickens are of egg-laying age, there beaks are cut off without any pain killers to ease the pain, they do this so the chickens don’t break their own eggs and eat them because the chickens are hungry. Broiler chickens, luckily for them, only live up to 7 weeks old until they are big enough to be slaughtered. Their life starts out in incubator trays with hundreds and thousands of other chicks without enough head room to stand up, and not enough room to take 2 tiny steps. So for the first week of their lives it goes from cramp trays, to cramp boxes, to getting dumped onto the filthy floors of t...

Film & Ideology – Milk

Assignment 2 – Film and Ideology The definition of the word ideology can be represented in many ways. Today’s basic understanding of the word can be defined as â€Å"the body of ideas reflecting the social needs and aspirations of an individual, group, class, or culture† (Farlex, 2009). Gus Van Sant’s exceptional biopic Milk (Gus Van Sant, 2008) depicts the story of Harvey Milk, the slain gay-rights activist who became the first openly gay man elected to any substantial political office in the history of the planet. Harvey Milk’s life changed history – his courage still motivates people today, his ideals still teach people today and his hope still inspire people today. The release of Milk in 2008 has helped to bring back a new sense of appreciation for the hope and passion that Harvey Milk died for. Milk beautifully shows the fights and struggles Harvey Milk had to go through to gain the trust of the people and in order for his ideologies of a brighter tomorrow for all queer people to be fully appreciated by everyone. Harvey Milk was an individual who did not die in vain; his efforts in fighting for gay rights left a lasting impact on the people of this planet and his hope still lives on to this day. Simply put Harvey Milk’s ideology of fighting on and instilling hope in the fight for gay rights when no one else would, immortalized him – â€Å"Without hope, life's not worth living† (Milk, 2008) It is now June 7th 1977, the sun has set on the Castro district of San Francisco, and the crowd that has gathered in the street outside Harvey Milk’s camera shop is becoming more and more, impatient and angry. We know watching that the reason that everyone is angry is due to the reports about voters in Dade County, Florida, having voted to overturn a local gay-rights ordinance, giving momentum to a backlash whose most visible public face belongs to Anita Bryant. We know we have reached the climax of the movie. So much is happening all at once in the life of Harvey Milk that you wonder how he has not yet lost his head. His impish upbeat attitude and overly positive optimism in the face of multiplying frustrations makes you look up in awe at the wonderment that is Harvey Milk. The gay residents of the Castro are angry and looking to Harvey for leadership. Though not yet elected to office and having lost 3 years consecutively, Harvey rises to the occasion and leads the angry crowd to city hall where he picks up a bullhorn and address the crowd in a way only Harvey Milk can – turning an angry mob on the verge of a violent riot to a enthusiastic mass willing to fight for their rights the proper way. In the space of a few minutes Harvey goes from a whisper to a shout, from an intimate message of consolation and support to a defiant public speech. Milk shows us that it is these moments, these distinct modes of address, are connected, and that the link between them is what defines Harvey Milk’s aspirations and ideals. According to Dr. Harry M. Benshoff, an associate professor of Radio, Television, and Film at the University of North Texas, queer theorist focus on how sexuality was and is a product of culture, not some sort of biological given. In Milk it is clearly stressed that Harvey too did not believe that homosexuality was a genetic disease. In the scene of the 1977 June 7th march, just before he leaves the store to lead the mob to city hall, Harvey answers the telephone only to be greeted by a scared and confused teenager whose parents believe him to be ill because he is gay. Harvey’s disregard of homosexuality as a genetic disorder is abundantly clear in this scene when he reassures the teenage boy that he isn’t ill and that being gay is perfectly normal. Dr. Benshoff goes on to day that following the work of Alfred Kinsey and Sigmund Freud, queer theorists argue that human sexuality—or indeed, race, gender, class, etc. are not either/or propositions, but are rather fluid and dynamic socially-defined positions. To suggest that there is one norm (straight white man on top sex for procreation and nothing else) is grossly misleading and only serves to foster rule by the same and persecution of everything else. Throughout Milk we can see that Harvey, though a very passionate gay-rights activist, is not only looking out for the queer folk. He holds dear to the ideal that everyone is equal. In a way he embodies what Kinsey and Freud say. He did not believe in just one norm. In his fight for gay-rights he isn’t trying to one-up the vast heterosexual majority by over throwing them and getting homosexuals to run the world, he is merely trying to get them to see that homosexuals are no different from any other person. Harvey Milk was trying to break down the social barriers that led to narrow minded thinking of just one social norm. In Milk during one of the public rally’s he had, Harvey said that â€Å"all men are created equal. No matter how hard you try, you can never erase those words† – he believed these words with all his heart. To Harvey Milk, he wasn’t just fighting for gay-rights; he was fighting for a way of life that did not constrict its citizens to conform to just one social norm. Milk, Gus Van Sant’s film project that was close to two decades in the making, was released on the 26th of November 2008 and marks the 30th anniversary of Harvey Milk’s death and the brief but brilliant political career he led. Harvey Milk was unfortunately gunned down on November 27th 1978, three weeks after his biggest political victory. The San Francisco city supervisor had been in office less than a year when he spearheaded a statewide campaign to defeat Proposition 6, a ballot initiative that called for the mandatory firing of gay teachers in California. Milk however arrived in theaters three weeks after the biggest political setback the American gay rights movement has suffered in years: the passage of Proposition 8, which reversed the California Supreme Court ruling that legalized same-sex marriage. As untimely as the events that unfolded prior to the theatrical release of Milk, it begs the question on how did Proposition 8 change the meaning—the symbolic and ideological significance as well as the real-world function—of Gus Van Sant’s Milk. The passing of proposition 8 transformed Milk from a delicate, serious-minded period biopic that was directed by the brilliant Gus Van Sant into something much more urgent. Milk was suddenly this shinning beacon of hope that reinstated the hope and passion that was Harvey Milk into today’s gay-rights activist. There are some moments in the film that in retrospect seem as though it is speaking directly to the audience of the present. As the Proposition 6 results start to roll in, Harvey tells his followers: â€Å"If this thing passes, fight the hell back. † Those eight words speak volumes to the people who are fighting against the proposition 6 of today, proposition 8. â€Å"Somehow, when 8 passed, something else happened that was even more intense than the campaign, which is good. It was an inspiring reaction that showed strength to the people who were against Prop 8. So yeah, it seems to have an effect on something that's similar to it: Prop. 6, that appears in our movie†, Milk director Gus Van Sant was quoted during an interview with IFC. com. The activist understood the message Harvey Milk stood for in the day, and opted not to let his valiant efforts go to waste. To judge from the numerous rallies that have sprung up across the country since Prop 8 passed, many gays and lesbians are doing just that, refusing to go down without a fight. Gay rights advocates have been quoted saying that they hope to capitalize on Milk's fortuitous topicality. The film's Oscar winning screenwriter, Dustin Lance Black, and veteran activist Cleve Jones published a manifesto for equality in the San Francisco Chronicle on November 14th 2008 and launched a nationwide campaign of mass protests and civil disobedience. The endnote of their manifesto read, â€Å"Remember always, and reflect in all your actions, that we are not fighting against anyone, or anything. We are struggling for equality†. Harvey Milk was the one that picked up the flag when no one else would. He was the one that led the suppressed minority on to recognition and acceptance. All who wear his badge, or speak his words, or hold strong to his ideals, keep him alive. Milk managed to revitalize Harvey and in a strange twilight zone sort of way enlisted today’s newly radicalized generation to find their figurehead in the movie-hero version of a long-dead hero. In Milk we see that Harvey’s main arsenal in his fight for equality was that he rejected secrecy and shame in favor of openness and visibility. He insisted that the fight against homophobia begins with the act of coming out – â€Å"If they know us, they don’t vote against us†. Harvey Milk realized this earlier than many of his contemporaries. He understood that in order to gain true equality gays and lesbians should serve as their own civil advocated instead of merely relying on pacts and promises made with their straight allies in high and powerful places. Though he was seen as a radical at the time, in retrospect Harvey Milk is an optimist, an idealist, a true believer in the possibilities of American democracy. Gus Van Sant understood where Harvey was coming from with his ‘come out of the closet ideology’. In the interview with IFC. om Gus Van Sant sheds some light on the ideology and how it affected him. â€Å"It was Harvey's one idea that would have worked and probably did help the â€Å"No on Proposition 6† campaign†¦ultimately, it's an interesting concept, and that was the way he thought had a huge effect on Proposition 6. If it's not an unknown, it's not scary. If it's a known, it's friendly and you understand, ‘Oh t hat person that I know is gay, and this other person I know is gay’. That's partly how it works†. The openly gay Hollywood director went on to say, â€Å"But people did come out. It was his drive to just come out of the closet, lock the closet, and stay out, which was followed by many people. And really, it was his death request. If a bullet should enter his brain, may it knock down every closet door — that was his last request, his will, which probably extended to many people, including me, because I came out after he was killed†. This is just one of the millions of example on how Harvey Milk’s ideals and aspiration for equality for homosexuals touched and affected the lives of many closeted ones. Milk’s screenwriter Dustin Lance Black was quick to praise Harvey Milk’s ‘come out of the closet’ ideal a really good solution to a problem that tons of people had diagnosed but had yet to offer any answers to in an interview with ABC Radio. In the same interview he said, â€Å"In the years that Harvey put that into place, that sort of philosophy into the campaign, he won an election and a month later he was able to defeat one of the biggest, most popular anti-gay pieces of legislation in our country. He was able to defeat it, very unexpectedly, with that philosophy†. The recent anti-Prop 8 movement however seemed to embrace the opposite tactic. It was a closeted campaign, devoid of a public face, largely dependent on straight spokespeople, and run with a wary defensiveness that would have driven Harvey Milk mad. The story and context of Milk, and of the times in which Harvey Milk lived and led, make clear the continuation of this struggle we still find ourselves in. As soon as you lose a battle, another one looms before, giving you another opportunity to try to win. You win a battle, and before you can catch your breath, another struggle is on the horizon. We fall down only to pick ourselves back up again. Nothing about progress allows for much in the way of rest, but nor does it allow for much to remain stagnant. Harvey Milk’s thoughts were ones that changed the world. His thoughts turned into full out ideologies and his ideologies in turn morphed into a revolution. The ever brilliant Gus Van Sant who has a certain knack for merging the lines between now and then delivers to us a biopic that brings back to life its subject. In the post-proposition 8 viewing of this film, we can now see the rise of a new generation of activist – ones that have been instilled with a new sense of hope. Just as Harvey Milk’s assassination, which he repeatedly foretold, has meant that he remains frozen in time as a martyr, the Proposition 8 result has, for now, has redefined Milk as a cause. Gus Van Sant’s 20 year long journey of bringing to life this culturally epic subject has cemented Harvey Milk’s position as an ideological leader. â€Å"Lives of great men all remind us; we can make our lives sublime, and, departing, leave behind us, footprints on the sands of time† (Longfellow, 1838). Harvey Milk’s footprints would have never been forgotten, but Milk has in a way reaffirmed this stand. Gus Van Sant brought about a hero that was long gone and risen him from six feet under to be celebrated again as if he was never gone. Harvey Milk believed in one thing above all else and that was hope, Gus Van Sant brought back that hope. â€Å"I ask this†¦ If there should be an assassination, I would hope that five, ten, one hundred, a thousand would rise. I would like to see every gay lawyer, every gay architect ‘come out’ – If a bullet should enter my brain, let that bullet destroy every closet door†¦ And that's all. I ask for the movement to continue. Because it's not about personal gain, not about ego, not about power†¦ it's about the â€Å"us's† out there. Not only gays, but the Blacks, the Asians, the disabled, the seniors, the us's. Without hope, the us's give up – I know you cannot live on hope alone, but without it, life is not worth living. So you, and you, and you†¦ You gotta give em' hope†¦ you gotta give em' hope. †, were the last lines of Milk. (2435 words) References: 1. Black, D. L. (2008) Interview with Dustin Lance Black, writer, ‘Milk’, viewed May 2009, 2. Doty, A. 1998) The Oxford Guide To Film Studies: Queer Theory, Oxford University Press Inc, New York 3. Dr. Benshoff, H. M. (2006) Notes on Gay History/Queer Theory/Queer Film, viewed May 2009, < http://www. unt. edu/ally/queerfilm. html> 4. Milk, 2008. Film. Directed by Gus Van SANT. USA: Focus Features 5. Sant, G. V. (2008) Interview: Gus Van Sant on â€Å"Milk†, viewed May 2009, < http://www. ifc. com/news /2008/11/gus-van-sant-on-milk. php> 6. TheFreeOnlineDictionary. Com By Farlex (2000) The American Heritage Dictionary of the English Language, Houghton Mifflin Company, Boston

Personal Narrative- Improved Writing Essay - 984 Words

My first real writing experience happened my junior year at HHS. It was the second to last day of school of my sophomore year, and I happened to be flipping through the course descriptions book, and was thinking of an English class to take next year. Well, I sat there and sat there thumbing through the pages, and finally, one particular class appealed to me. I thought, WOW, this is a class I should take! Yeah right, but I still decided to register for American Lit.anyway. Well, the school year finally ended, and I wasn’t too happy for next year’s school year to begin. I mean, American Lit. was going to be boring with all the reading, not to mention all the writing, too. But I didn’t consider the writing to be a big problem,†¦show more content†¦course to us. And let’s not forget about grading either, she said. I barely even heard her, though, because I was trying to sleep. Then she talked about reading, which was alright, I guess. 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