Kirtrines Basement :: Personal Narrative, Autobiographical Essay

Kirtrines Basementbaby Lopez? I looked down the winding staircase into the murky depths of my neighbors unfinished basement. Sister Lopez, can I talk to you?The and sound was the steady hum of the sewing machine, so I quietly took the stairs two at a date. I was twelve years old--polite and refined, simply not overly patient. My mother, a wonderful but slightly overzealous Mormon Relief Society president, had sent me with a Homemaking invitation to give to the forever-elusive, inactive Sister Lopez.Sister Lopez was sitting at a large table, feeding canvas into a huge sewing machine. The only light in the room was the left(predicate) sun that managed to squeeze through the window well. It illuminated her hair which fell to her shoulders like blackberry sit downin. I watched her look up at me with only crackers curiosity. Hello.Hello... I wanted to give you this.Thanks. Why dont you sit down? Her face was so flawless, so unreal. She looked like a woman in one of my mothers catal ogues--Lands End, maybe, or J Crew. I took a folding chair from its resting place on a cement wall. How are you, Sister Lopez? I asked. It was all I had ever been taught to ask an adult. Sister Lopez laughed the most sincere laugh I had ever heard. I suppose it was the laugh of a jubilant woman, but at the time I wasnt familiar enough with laughter to tell. Call me Kirtrine.Kirtrine. I liked the way the word sounded on my lips.And the real question is, she continued, how are you?To say the least(prenominal) I was startled. Me? Im fine. As if anyone needed to ask how I was it was perfectly apparent to any semi-competent onlooker. I was almost thirteen, with matted brown hair, awkward, angular glasses, and an uncomfortable clog gain where hips should have been. A pubescent nightmare, I had acne like the before picture on a skin care infomercial and crooked teeth, sure enough the envy of every jack o lantern. How was I? I was a mess.Tell me about school, she prodded, though it sound ed like anything but prodding.Any cute guys?I sat there, on a cold, hard folding chair, surrounded by bolts of colorful cloth. I opened up like I never had before in that room I cried with the ice blue chiffon, I laughed with the tomato red flannel. I was as pristine as crisp white linen I was as sophisticated as black velvet.

Analysis of Shakespeares The Tempest - Racism :: free essay writer

Racism in The Tempest     One manifestation of racism that Cesaire surfaces is the proliferation of negative opaque stereotypes. Cesaire uses Prospero to expose the feeble, racist stereotypes many Whites propagate about Blacks. Prospero, presenting a common White opinion, says to Caliban, It Calibans living quarters wouldnt be such a ghetto if you took the trouble to keep it refreshed (13). Such a statement is clearly racist and plays into the stereotypes many Whites bear about Blacks (i.e., they are lazy and dirty). These stereotypes are White lies. The cleanliness of a residence has truly little to do with whether it is a ghetto or not. Also, Prosperos stereotypical response puts the blame on Blacks for problems that were ultimately created by European colonization and the subsequent employment of Africans as slaves. Furthermore, it can he argued that Whites are the lazy race because they are the ones who initiated African slave labor. Another stereotype that Whit es often impose on Blacks has to do with a Black mans supposed desire to have sex with White women. Cesaire addresses this issue when Prospero accuses Caliban of trying to rape his daughter(l3). Cesaire is pointing out a classic case of White antheral guilt projection. History has clearly shown that more White men, supposedly pious slave owners in particular, have taken advantage of Black women, than Black males have of White women. The historical White power structures in America have facilitated the circumstances that have made this kind of sexual exploitation of Black women possible. By using Prospero to accuse Caliban of laziness and sexual impropriety, Cesaire poignantly reveals the hypocrisy of Whites.   Another manifestation of racism that Cesaire draws to our attention is the woefully inadequate educational opportunities that exist for Blacks in America Caliban indicts Prospero when he says, as for your learning, did you ever impart any of that to me? No, you took care not to. All of your science you keep for yourself alone, shut up in those larger books (12) While such a statement is historically accurate in the sense that Whites sought to keep Black slaves uneducated so that it would be easier to ensure them, the statement also addresses the more subtle, but no less evil, form of educational racism that still exists to this day. Jonathan Kozol paints a graphic picture of degrading despicableness when it comes

Land Travel in the 17th Century Essay -- European History Essays

Land Travel in the 17th CenturyBarbara Blaugdone travelled a great deal, using her faith and drive to spread her message across England and Ireland. In England, she traveled well over a hundred miles, in Ireland she traveled over two hundred. She also made several voyages by sea. Her travels must have been long and difficult, as she faced non only the everyday dangers of the thoroughfare but the dangers of persecution and imprisonment as well. Many Quakers traveled in her time, following Gods will and spreading their message across many miles. They were not the only ones who traveled by land, however. Merchants and businessmen depended on goods, which were transported to them by farmers, merchant caravans, or ships. Peddlers made their living by travel, selling various goods and buying others. monied young men often traveled to complete their education, and members of the upper-class visited health spas. Mainly, land travel was on foot or in the saddle. In plus to their own t wo legs, lower classes relied on mules or asses, wagons, and hand carts. The upper class used h...

Woodstock 1969 Essay -- essays research papers

Woodstock 69Many large concerts occurred throughout America in the summer of 1969, but none were as hale known and symbolic as Woodstock. Its message was clear three days of Peace and Music. Its impact on Americas culture and society as well as its youth will not be forgotten for many years to come. Four workforce named Michael Lang, Artie Kornfield, John Roberts, and Joel Rosenman originally established Woodstock. The mens initial idea for the festival was to promote the idea of a new recording studio in Bethel, New York, which is where the event actually took place. (Jacksonville.net) Because of the elongated amount of rain that fell before and during Woodstock, the site was changed twice and halted up on Max Yasgurs farm. (Bethelwoodstockmuseum.com) This resulted in the loss of preparation time. The tip had not been entirely put up and the sound system was dangerously assembled. There were many other(a) problems that occurred as a result of the mud produced during the rain. nigh of the gates and fences were not put up which allowed many mint to enter the festival for free.(Jacksonville.net) The mud also created a major cleanup project aft(prenominal) the festival ended.Woodstock gathered an unexpectedly large attendance. Only 50,000 to 100,000 people were expected to arrive at the site. These numbers seemed small compared to the 400,000 to 500,000 people who converged on the area on August 15, 16, and 17 of 1969. (Websters) Many expected singers and bands could not arrive due to traffic backed up for miles along all the roads leading to the area. It was state that nearly one million people could have attended the concert if it had lasted longer. (Visi.com) Many recognized melodyians preformed at the concert such as Janis Joplin, Jimi Hendrix, Creedence Clearwater Revival, The Who, Jefferson Airplane, and many others. (Home.columbus.rr.com) in truth by the first day, as the musicians looked out upon the vast crowd, they must have known that Woodst ock was not going to be just another concert that would be forgotten. On the outside, Woodstock could just be considered another concert for the youth of the time to hear their favorite music, but it can be seen that it was much more than that. Although the music was a large part of the festival, there would be no reason for it to be remembered this long if that w... ...stock fans that made the trip to all three festivals bearing the Woodstock name. It seemed that the other men and women that made up the rest of the audience were nearly all there to get drunk and destroy anything they could get their hands on. By the end of the concert, nearly all of the stage and equipment was destroyed. Women were raped and all souvenirs such as shirts and posters were stolen. (MTV Woodstock Uncensored) The acts displayed at Woodstock 99 could be summed up in two words soul-destroying force. It went beyond misguided violence to such a point as to bring down some of the original Woodstocks glory. Unfortunately now when people think of Woodstock they will also think of the destruction that occurred during its latest attempt at recreation.Despite peoples desire to bring back the belief of the original Woodstock, all that can remain is its effect on the people who experienced it and the affect on the culture they lived in. The concert was necessary to have because it alleviated tension in a time of history that was full of war and prejudices. Its stories will be told, some good, some bad, but the desire that people smell out to experience it firsthand will never be lost.

Christof Koch and the Theory of Consciousness Essay -- Consciousness

Consciousness was first described and introduced by Sigmund Freud and Friedrich Nietzsche (Crick & Koch, 2001). It has been described as a realm of the mind that controls human behaviour. However consciousness is not cordial to conscious introspection, self-examination or a source of knowledge. On the contrary, Christof Koch, a neuroscientist collaborator of Francis Crick, describes insensibility as any neuronal activity that does not bring out rise to conscious sensation, thought or memory (Crick & Koch, 2001). Though unconsciousness differs in many different ways to consciousness, it works in a waking state that deals with cause and effect and the logical spontaneous processes in order to process information. On the contrary unconscious mind is associated with involuntary activities that form connections with thoughts, ideas and reflections, which unconsciousness also has the capability for multi-tasking. Therefore, as Koch explains, unconscious puts humans is an online mode, a llowing us to override our instinctual offline programming.Scientists and philosophers have different understanding and explanations for consciousness, as it used to be observed from a philosophical point of view only. However, the advancement of technologies in understanding brain from a computational, bio-molecular and cognitive and behavioural flack, consciousness is being studied from a neuroscientific approach as well. Therefore neuroscientists have difficulties in verifying and understanding its existence, for example, Dennet believes consciousness is the evolved capacity for self-knowledge that gives us the subjective experience. Where as Francis Crick looks at from a all neuroscientist view that one should look at Neural Correlates ... ...Natural Correates of Conscouness (Cambridge, MassMIT Press, 2000) NCC. Retrieved 29th of December 2011Reagan, Leslie A., et al, ed (2007). Pavlov Children Medicines moving pictures. Rochester, NY University of Rochester Press. p. 285. Re trieved 7th of December 2011Scheff, Thomas Ph.D. 2009. Emotional/ comparative World. Psychology Today. www.psychologytoday.com. Retrieved 2nd of December 2011.http//www.psychologytoday.com/blog/lets-connect/200909/the-emotionalrelational-worldShear, J., Explaining Consciousness The Hard Problem (Cambridge, Mass MIT Press, 1997) (and Journal of consciousness studies 1995)Tsuchiya & Koch. (2009) Tsuchiya, Naotsugu. Koch, Christof. The relationship Between Consciousness and attention. Chapter 6. The Journal of The clinical neurology of Consciousness. www.klab.caltech.edu. Retrieved in the 2nd of December 2011.

Christof Koch and the Theory of Consciousness Essay -- Consciousness

understanding was first described and introduced by Sigmund Freud and Friedrich Nietzsche (Crick & Koch, 2001). It has been described as a realm of the mind that controls human behaviour. However cognizance is not accessible to conscious introspection, self-examination or a source of knowledge. On the contrary, Christof Koch, a neuroscientist collaborator of Francis Crick, describes unconsciousness as any neuronal drill that does not give rise to conscious sensation, thought or memory (Crick & Koch, 2001). Though unconsciousness differs in many different ways to consciousness, it works in a waking state that deals with cause and effect and the logical spontaneous processes in order to process information. On the contrary unconscious mind is associated with instinctive activities that form connections with thoughts, ideas and reflections, which unconsciousness also has the capability for multi-tasking. Therefore, as Koch explains, unconscious puts humans is an online mode, allowin g us to override our instinctual offline programming.Scientists and philosophers have different understanding and explanations for consciousness, as it used to be observed from a philosophical point of view only. However, the advancement of technologies in understanding brain from a computational, bio-molecular and cognitive and behavioural approach, consciousness is being examine from a neuroscientific approach as well. Therefore neuroscientists have difficulties in verifying and understanding its existence, for example, Dennet believes consciousness is the evolved capacity for self-knowledge that gives us the subjective experience. Where as Francis Crick looks at from a completely neuroscientist view that one should look at Neural Correlates ... ...Natural Correates of Conscouness (Cambridge, MassMIT Press, 2000) NCC. Retrieved 29th of December 2011Reagan, Leslie A., et al, ed (2007). Pavlov Children Medicines moving pictures. Rochester, NY University of Rochester Press. p. 285. Retrieved 7th of December 2011Scheff, doubting Thomas Ph.D. 2009. Emotional/Relational World. Psychology Today. www.psychologytoday.com. Retrieved 2nd of December 2011.http//www.psychologytoday.com/blog/lets-connect/200909/the-emotionalrelational-worldShear, J., Explaining Consciousness The Hard Problem (Cambridge, Mass MIT Press, 1997) (and Journal of consciousness studies 1995)Tsuchiya & Koch. (2009) Tsuchiya, Naotsugu. Koch, Christof. The relationship Between Consciousness and attention. Chapter 6. The Journal of The Neurology of Consciousness. www.klab.caltech.edu. Retrieved in the 2nd of December 2011.

Midsummer by Manuel Arguilla

- TANCIOCO, MICAELA A. 12/13/11READING LOG 1LIT02 Midsummer by Manuel E. Arguilla The story is roughly Manong whom had encountered a girl in the mid-day of summer. At first he didnt saw the girl. When he saw her, he got curious and started following her everywhere she go. every detail on what the girl is doing was noted in the story. By the way she got the jar placed in her head and etc. He then portrayed what the schoolgirlish madam look like. He left the bull and his cart in the road as he followed the young lady.As the young lady does her thing, the boy continues his journey and lunch came. He then rest and waited in a path where he know the young lady will pass. After both(prenominal) time he waited until the lady was there and offered the lady the lunch he have. The lady didnt answer and smiled at him at first. But then the young lady told him that she finished her lunch already thats why shes getting some water in the middle of the day. They became acquaintances and start ed chatting about stuffs.The girl share that all they have as food is salt and rice that made Manong shocked. The young lady offered Manong to go to their house but Manong insisted. The young lady alleviate wants Manong to go to their house so Manong decided to go because he got no house to sleep for the night. Manong did realize that he wants to know the true person in that young lady he met this afternoon and with that his last words was He felt that he could follow the lender, lithe figure ahead of him to the ends of the world. I depend Manong felt love that instant she met the young lady. With him only looking for a distance made his heart grow fonder. It made an urge to know much about the young lady. With the young lady offering their home to this stranger made a good implication to Manong that he had an idea that this young lady had a good heart. He then realize after the end of the day that he fell in love with the stranger he had met awhile ago. That he can go where eve r as long as he is with this girl.

Psychology and Social Support Essay

Marriage these days does not seem to last truly long. Two months after his wedding, your friend Tom confides in you that hes unhappy in his marriage. He tells you that he and his wife seem to be scrap all the time, and nothing seems to get resolved. He tends to be very high-strung anyway(His friends call him Type-A Tom) and now he feels like the focussing of the constant brabble is affecting every aspect of his life, including his health. Since youre in a Psychology class, he asks you for your thoughts on the chances of his marriage surviving and your advice about what he can do about his stress.Based on what youve read (either in the assigned readings in this module or your own Internet research), you answer his questions by addressing 10 factors that whitethorn be related to his situation. Briefly discuss each of these factors (and how it may relate to Toms predicament) in a 5-7 page essay.The Factors arePredictability of the stressor. In psychology, stress is a feeling of str ain and pressure. Symptoms may include a sense of being overwhelmed, feelings of anxiety, overall irritability, insecurity, nervousness, social withdrawal, loss of appetite, depression, panic attacks, exhaustion, high or busted blood pressure, skin eruptions or rashes, insomnia, lack of sexual desire (sexual dysfunction), migraine, gastrointestinal difficulties (constipation or diarrhea), and for women, menstrual symptoms. It may also cause more serious conditions such(prenominal) as heart problems. Also, experimental research which has been performed on animals, also displayed results relating to stress and negative effects on the body. It has been shown that stress contributes to the initiation and development of specific tumors at heart the body.A stressor is any event, experience, or environmental stimulus that causes stress in an individual.22 These events or experiences are perceived as threats or challenges to the individual and can be either physical or psychological. Rese archers have found that stressors can make individuals more prone to both physical and psychological problems, including heart disease and anxiety.23 Stressors are more likely to affect an individuals health when they are chronic, highly disruptive, or perceived as uncontrollable.23 In psychology, researchers generally screen out the different types of stressors into four categories 1) crises/catastrophes, 2) major life events, 3) daily hassles/microstressors, and 4) ambient stressors. companionable support (human relationships) Social support is the perception and actuality that one is cared for, has assistance available from separate people, and that one is part of a supportive social network. These supportive resources can be emotional (e.g., nurturance), tangible (e.g., financial assistance), informational (e.g., advice), or companionship (e.g., sense of belonging). Social support can be measured as the perception that one has assistance available, the actual received assistan ce, or the degree to which a person is corporate in a social network. Support can come from many sources, such as family, friends, pets, organizations, coworkers, etc. Government provided social support is often referred to as Public aid.

Organisational dialogue

First, this essay will explore the definitions of conversation as well as organisational stopping points and how these concepts related to each other. It is followed by a discussion on the ways that discourse may have positive effects regarding the cultural aspects. The terminal section of this essay pays attention to the challenges of and solutions to implementing and promoting dialogue within an organization. There Is a variety of deflations of dialogue.The derivation of this word stems from the Greek roots dialogs which consists of did and logos. Did factor through, and logos means the word, or more than specifically, the meaning of the word (Boom 1996, p. 6). Based on its origin, Boom (1996) defines dialogue as a combination of communication practices flowing through and among people, focused on discovering the essence and power of people thinking and how the groups acculturation is built through this process.Isaacs (1999) believes that dialogue Is, In particular, a flow of meaning, while Gerard and Eleanor (2001 ) define dialogue by contrasting It with discussion and conclude that dialogue is seeing the whole and connections between arts, learning through asking and answering, and creating shared meaning among group members. In tho similarities, Gerard and Turfs (1995) assume that dialogue is concerned with the environment where belief and communication diversity are encouraged In terms of respects, honors and set, as well as sensation to raise the creation of shared meaning.The role of dialogue in relation to organizational finish is of thorough understanding through many deferent organizational culture definitions. In fact, we all comm only(prenominal) think that it is the way we do things nigh but through research of organizational behavior, Machines, Lessons & Traveling (2013) believe it consists of values and assumptions shared within an organization (p. 448). At the same beat, for E. C. Martins and F. Turbulence (2003), the central Ing redient of culture Inside an organization is the subconscious shared values and beliefs.A powerful culture offers shared values that ensure everyone in the organization focus on the same goals and objectives (Robbins, 1996). Organization has its culture usually performs higher in the market. In a word, the key bluster of building and transforming organizational ultra Is creating and maintaining shared values that expect to be the main purposes of outlining dialogue among members. Through practicing dialogue, collective communication is created, and organizational culture is transformed. These aspects include transformation of member behavior, the experiential feeling of companionship and peoples attitudes.Firstly, in the comparison between dialogue and discussion of Gerard and Eleanor (2001), the main role of dialogue is to help people learn how to communicate with each other differently and produce collective understanding. While in discussion, people intend to keep their opinio ns and only the most powerful and influenced person might decide the results of the whole group, dialogue, in contrast, gives members a commitment to a common set of guidelines (Gerard and Turfs 1995). Participants try to minimize conflicts and add together all different points of view into a standard value.Therefore, the more often people practice dialogue, the more behavioral changing they have to integrate and begin in community. Moreover, based on Bombs research in 1996, Isaacs (1999) stated four principles of dialogue which include minding, respecting, suspending and voicing. Among these principles, audience skill plays an important role in changing behavior of a group. As a whole song could not be sensed and understood through a single note (Isaacs 1999), organizational cultures and objectives are not able to be established by a single idea.Hence, dialogue is a powerful tool to encourage people to listen thoroughly to others ideas and engage in the conversation. Then, sha red meanings, or the culture of the company is gradually transformed. Secondly, by setting up the conditions of community, dialogue transforms the feeling of the corporation culture (Gerard and Turfs 1995). When a new group starts to involve in the community, dialogue will generate an atmosphere having the experiential feel (Gerard and Turfs 1995, p. 148) of community.In an organizational scope, employees commence to sense what the companys culture would seem to be in full community based on its principles. Furthermore, for Sense (1995), dialogue is as a facilitator for team learning. He believes that team is the key feature to create shared values, and through the application of dialogue into team learning process, knowledge and feeling of the community cultures are transferred from one to others, ND individuals values as well as beliefs are positively transformed and integrated into the collective cultures.The final aspect that dialogue has the power to change the organizational c ulture is attitudinal transformation. As participants experience the effects of dialogue, the attitude level becomes as a byproduct of the incorporation of new modes of behavior and learning the feel of what being in community is like (Gerard and Turfs 1995, p. 148). Then, cooperative and collaborative attitudes start to replace the attitudes of inflexible individualism. This statement is conformable with the research f Scheme (1993) where he describes dialogue as talking around the campfire (p. 391).During the past time, meetings were usually held around a campfire where people could simply share their opinion without any discussion or arguments. Through that, (Scheme 1993) and spend time listening to others opinions before reflecting on their assumptions. Moreover, Isaacs (1999) also emphasized the main goal of the respecting principle of dialogue that is not to seek a decision, but to tolerate difference, gap and conflict. Therefore, the more people practice dialogue, the more he y have collective orientation by gradually changing their individualistic behavior, and then, the whole organizational culture is enhanced.Although dialogue has been proven to have a positive effect on organizational culture, people still face challenges in applying it into organization learning system. First, most organizations are in general a hierarchy and authorized social organisation which is contrary to the principles of dialogue (Boom, 1996), so employees tend to afraid of expressing their ideas or opinions to the people who are at higher level. In fact, in some top-down companies, managers have the right to create and change organizational culture as well as enforce rules and delegate duties to employees.Although it has its value, this structure might find it difficult to get dialogue going. Moreover, there are situations where people have different ideas and assumptions, and dialogue might become frustrated. If someone is not willing to listen to others assumptions, it i s considered as an act of violence (Boom, 1996) which may lead to an argument and no results could be concluded. And last but not least, in moorage of a cross-culture organization, dialogue becomes a more complicated and lengthy Scheme 1993) process due to the different cultural backgrounds of the employees.Then, it is necessary for companies to allocate more time and resources in designing dialogue process that may help employees communicate effectively, and the organizational culture is transformed on the right track. Despite all these challenges, dialogue still plays a significant role in transforming organizational culture if companies have methods and strategies to apply it appropriately. Sense (2006) gives a simple analysis about match dialogue and discussion within members of an organization. As in a discussion, decisions are made.In a dialogue, complex issues are explored (Sense 2006, p. 230), learning team must learn how to cut back movement back and forth between dialog ue and discussion and distinguish between the ground rules and the goals to have both dialogue and constructive discussion. Communication audited account is another approach to deal with the organizational practice of dialogue. For Harrier and Tourist (2004), communication audit is the key to creating a world-class communication system since the results of communication performance among all staffs is accurately reported to the managers.This process is effective to solve problems both in top-down organization and cross-culture since it reveals communication strengths and weaknesses among employees at all levels as well as suggests solutions for improvement. In conclusion, dialogue has proved itself as an effective but challenging way of transforming organizational culture. Through behavioral, experiential and attitudinal transformation, corporation culture is positively changed as dialogue awareness of the collective assumptions, minimize arguments and by practicing dialogue, peopl e learn how to accept the differences of others.

Historical Report on Race Essay

A life that we thought was best for us and our kids to bugger off up in. We produced our own food, shelter and weapons and provided for ourselves in the most natural way possible. It wasnt forever and a day easy though, and others seen more value out of our land and resources than us. I was forced off my land and had to adapt to the new peoples way of life. That in which they called a white society this society created many acts in my life quantify in order to weaken our society much(prenominal) as those of the Allotment Act and the Reorganization Act (Schaefer, p. 47, 2012). People of my cultural lived on reservations, we had learned to get out ourselves and adopt our own way of life and government. autochthonal Americans had created their own nation and it caused and has caused a lot of tension between us and the U. S. nuance. As a aborigine American, we were all about live the traditional way of life. There was value to our land and the resources that we used and the white people wanted and did take it from us.It seemed as if we were ever at war with the white people so that we could protect what we thought was rightfully ours. They had created an act known as the Indian Removal Act, which was passed in 1830 (Schaefer, p. 150, 2012). This overt more land for settlement and allowed people to come in and take over our reservations (Schaefer, p. 150, 2012). In 1946, Congress had created the Indian Claims Commission (Schaefer, p. 150, 2012). This was a good involvement for us, or so we thought. It meant that finally our voice was going to be heard.There were three members apart of the commission, and they were given a five year deadline, but in that location kept getting extension after extension, until in 1978 the whole thing was abolished (Schaefer p. 155, 2012). At times, it seemed as if maybe the government was try to help us, that or they were seek to use us. In 1952, the BIA began programs, so that they could relocate young Native Americans to Urban areas and by 1962 they had created what was called the Employment Assistance program also known as the EAP (Schaefer, p 157, 2012).Basically there primary goal was to relocate us by offering us better jobs opportunities that, that of the reservation could not offer. But this plan had curtly backfired on them. By 1965, one-fourth to one third of the people in the EAP had returned home to their reservations (Schaefer p. 157, 2012). Today, most of our land has been taken from us and no longer exist. Native Americans themselves are not being treated as badly as we were back then, but its the culture and our name that continues to be insulted. Schools have such a thing as mascots, and they create names for them.They use those such as the Braves or Redskins. Those names have a meaning to the Native American culture, it tends to bring up the past for us, and though there intentions may not be that of insulting us, some of us wear upont like it alike much. It hasnt always been ea sy for us, and at times I wanted to give up. But everything seems to turn out for the better. Ive learned that every culture and person has their own way of living and when someone sees a greater value of that persons living then they have to have it.Things dont always have to be that way people can come up with their own greater value of living. Remember, you dont always have to have someone elses greater value to have a greater value of your own. Make an even better living for yourself than trying to take someone elses. I hope you learned well from this letter and I wish you the best. Your Friend Resources Schaefer, R. T. (2012). Racial and Ethnic Groups (13th ed. ). Retrieved from The University of Phoenix eBook Collection database.

Parental Involvement, Poverty, and Student Achievement Essay

Current education reform is intended to influence higher(prenominal) student achievement. According to Hanushek (1997), the development of shoal reform is hulkyly do by economic issues. Education reform becomes a meaningful topic on the national agenda when the National Commission on Excellence in Education issued a constitution, A Nation At Risk (1983). This report foc substance abused on the claim that a steady increase in mediocrity had overcome schools which impacted upon the economic competitiveness of the country.One example of this competitiveness was when the Soviet Union 1957 launched Sputnik. It was concluded that declines in educational performance were in large part the result of inadequacies in the way the educational bring was conducted. The findings that fol let loose, selected from a much more extensive list, reflect four important aspects of the educational process content, expectations, time, and teaching. The United States government responded by beginning ref orm of how its educational system.As part of this process, all segments, including parent committees, were formed to give attention to the implementation of the recommendations of the report. The report further stated that reform should not only come from students, teachers, school boards, colleges and universities, local, state, and federal officials, teachers and administrators organizations, only when similarly from parents themselves with interested in and responsibility for educational consequence begin with the parent.Moreover, you bear a responsibility to participate actively in your childs education. You should encourage more diligent study and discourage comfort with mediocrity and the attitude that says let it slide, monitor your childs study encourage good study habits encourage your child to take more demanding rather than less demanding courses nurture your childs curiosity, creativity, and confidence and be an active participant in the die of the schools. Above a ll, exhibit a commitment to go on nurture in your own life.Finally, help your children understand that excellence in education cannot be achieved with off intellectual and moral integrity coupled with hard work and commitment (p. 26) Henderson and Berla (1994) did extensive interrogation linking agnatic familiarity to student achievement. There are a variety of parenting practices that absorb been associated with positive student outcomes. Despite this research, Desimone (2001) contends that in that location is still no clear understanding of how patterns and effects of parental mesh differ across ethnic and income groups.Previous studies have shown that parent function patterns go away according to parental social, racial-ethnic, and economic characteristics (Catsambis & Garland, 1997), but the findings have been mixed. Several studies have reported that low income minority parents often have different beliefs about parents utilization in school fight are less involved in school activities than higher income, non-minority parents (Delgado-Gaitan, 1991 Chavkin & Williams, 1993). Other studies, however, have demonstrated that the level of parent involvement by race-ethnicity (i. e., Asian, African-American, Hispanic, and white) differs for only a few types of involvement and that minority parents have higher levels of involvement in certain areas than do white parents (Catsambis & Garland, 1997). Previous studies have reported that low-income minority parents often have different beliefs regarding parental roles in school involvement and are less involved (Chavkin & Williams, 1993). Comer and Haynes (1991) have hypothesized that low income and inner city minority students may be more positively affected by certain types of parent involvement than other students.According to them, in order for parental involvement programs to be successful, they need to be focused upon a school improvement process that is designed to create positive relationships th at go for the total development of children and not the traditional bureaucratic or authoritative school environment which is a less collaborative structure. Other theorists (Devaney, Ellwood, and Love, 1997 Lewit, Terman, & Behrman, 1997) suggests that parental involvement may not be as effective in improving student achievement for low income children as for children from middle class homes.Because the large twist of risk factors that impact upon children living in poverty, including health, safety, and housing, the role of parental involvement in schools in explaining academic outcomes for those children may be significantly less than for their peers who do not experience as many negative environment influences. Desimone (2001) suggests that race-ethnicity and other background characteristics can be strong mediators in the effects of various types of parental actions and the impact they have on student achievement.While work in this area is limited, there is little information that compares the effects of multiple forms of parental involvement across several racial/ethnic and income groups. McNeals (2001) study investigated the relationships between parent involvement and socioeconomic status. Findings indicated that parental involvement was an important factor in explaining behavioral outcomes (such as truancy and dropping out) but not cognitive outcomes (such as science achievement), with the greatest support for parent child discussion and involvement in parent-teacher organizations.He contends that there have been inconsistencies with the findings linking parental involvement to academic achievement. The contradictions likely were related to one of the following weaknesses in research. The first condition was the use of perception measures by teachers rather than direct reports by students and/or parents. Another was a failure to fully conceptualize parent involvement into its constituent parts. The defy was not fully assessing the extent to which pa rental involvement differently affects academic achievement by social class.The three shortcomings can be improved upon but parent involvement has little effect on student achievement because it is a cognitive outcome and parental involvement affects behavioral outcomes. Reginald Clarks research shares findings from a body of research on closing achievement gaps in urban school communities (Ferguson, Clark, & Stewart, 2002). In Clark documents the importance of five influential factors for improved students achievement, especially among disadvantages urban students.The first factor is described as the teachers expectations and actions in the classroom. The second is amount of students periodic participation in high-yield in and out of school activities. High-yield out of school activities accept leisure reading, writing, studying, and participation in community and school clubs or programs, and playing organized sports. High-yield in school activities include participating in clas sroom lessons as well as structured leisure activities. The third factor is the quality of students participation in and out of school activities.The fourth factor is parental beliefs and expectations. The fifth factor is parent-teacher communication. Ferguson, Clark and Stewart, 2002 base that the type and amounts of constructive in school and out of school learning activities contribute to a success-oriented lifestyle. More specifically, Clark found that high achieving activities. Some examples of actions in the classroom include reading, working alone on a lesson, listening to a lecture, solving a problem with classmates, or asking questions.Ferguson, Clark and Stewart, 2002 found that high achievers spent more time during out of school high-yield learning activities than low achievers. Some activities include weekly time dialoguing with adults, hobby or volunteer activities, or organized sports. Regular study and homework routines, with adult monitoring or support, and reading and writing activities also were seen as practices in the home. Some less structured or unstructured activities include hanging out, playing video games, talking on the telephone, and watching television.Ferguson, Clark and Stewart 2002 found that the beliefs and attitudes of parents had a significant role in student success in becoming competent readers. The analysis of data from parents of 459 students about their expectations for their childs learning and their perception of whether they had been supported by their childs teacher showed that students benefit when parents set high standards for their childs performance in school and looking personally supported by partnerships they have formed with their childs teacher.Lastly, Clark indicates that parent beliefs are likely to be influenced by parent-teacher communication. In other words, parents may benefits from well-organized teacher-led communications. When teachers take specific actions to cultivate instructional partnerships with parents, those parents are more likely to support their childrens learning at home. Clarks data showed that students scores were higher on the Tennessee Comprehensive Assessment in reading when teachers reported more communication with parents.REFERENCES Bankston, C. L. , & Caldas, S. J. (1998). Family structure, schoolmates, and racial inequalities in school achievement. Journal of Marriage and the Family, 60, 715-723. Braswell. J. S. , Lutkus,A. D. , Grigg,W. S. , Santapau, S. L. , Tay-Lim, B. , & Johnson, M. (2001). Subgroup results for the nation and the states. In The nations report card Mathematics 2000 (pp. 53-181). Washington DC U. S. Department of Education, Office of Educational Research and Improvement, National Center for Education Statistics.

Coca Cola Research Essay

3.3 Collect and review entropy using appropriate methods, including primary and secondary research techniques The researcher utilize the questionnaire method as his primary research technique. The take after questionnaire was adapted from a previous research done by an Advertising agency regarding forte of advertize. This survey was then distributed online to a sample population within Metro Manila.And the secondary research technique that was used was from the study of Mr. Honorata Ocampo Lee which is about Comparison of the effectiveness of the physical distribution processess and strategies of Coca Cola bottlers Philippines Inc. and Pepsi Cola products Philippines Inc. in selected districts in Manila for the year 2001-2003.3.4 Analyze and interpret appropriate qualitative and quantitative data Quantitative research uses a scientific approach the researchers hypothesis which stated in his study willing need to bewilder an essay in proving and disproving that hypothesis. The data that will be generated can be analyzed mathematically. (Primary and Secondary research) The researcher used questionnaire to Qualitative research is concerned with the opinions and feelings the data that will be collected is not necessarily set of numbers. It looks at the overall image rather than the separate components. (Primary and Secondary research) 4.1 Record findings in an accepted coiffe and 4.2 Present and summarize the findings using suitable methods 1. Please open the link to view the ad strong. Have you seen this advert before? http//www.youtube.com/watch?v=oiu9PcEyQ5Y? Among the 50 respondents, 40 part (20 respondents) said yes and 60 percent (30 respondents) said they experiencent seen the advertisement yet.2. How would you rate the overall quality of this advertisement? 40 percent of the respondents thought that the advertisement was good. 32% answered fair, 16% answered very good, and 12% answered excellent. None of the respondents answered poor. The data suggests that bulk of the respondents thought of the advertisement as good enough or slightly higher up average.3. How would you rate this advertisement compared with the others youve seen with familiar products/services? Majority (64%) of the respondents answered that the Coca-Cola advertisement was just about the same as other products advertisements. Meanwhile 20% answered that their ads were A Little Better than the Others and 8% thought that it was much better than the others. On the other hand 8% answered that the advertisement was a little worse than others. This data shows that, like the previous analysis, the Coca-Cola Open Happiness advertisement comes across to the majority of the viewers as just average or slightly above average.4. Are You Currently Using This ProductA majority of the respondents (86%) said to be presently drinking Coca-Cola meanwhile 14% claimed that they are not currently using Coca-Cola.5. After seeing this advertisement, would you want to buy thi s product? A majority (95%) of the respondents were still determined to buy the product after seeing the advertisement and 5% said that they would not want to buy the product. Up by 9% from the people who claimed to not have been using Coca-Cola at the moment, the data shows that the advertising has given an impact only to a small amount of respondents to buy Coca-Cola. However, the data in like manner shows that regular consumers are still willing to purchase Coca-Cola plane though the advertisement did not come out that strong, as shown from the results in the second question.6. Have you ever used this product?The chart below shows that nose candy% or all of the respondents claim to have used or bought Coca Cola at one point in their lives.7. AgeAmong the 50 respondents, 30 (40%) were within the ages 18-25, 8 (16%) were 26-30, 12 (24%) were 31-35, 5 (10%) were 36-40, 3(6%) were 41-45, and 2 (3%) were 46-50.8. GenderThe chart below shows that majority (68%) of the respondents ar e male and 31% are female.4.3 Evaluate the methodological analysis used and critically analyze the findingsThe researcher used the Questionnaire method. This method was chosen because using a questionnaire with a random sample is a good focus to find out the attitudes, thoughts, and behaviors of a large group of people.The questionnaire that was used contained Close-Ended Questions. A set of choices was given to the respondents for them to be able to answer the questions. Aside from that, the researcher also chose to use Likert-Scales as this would be the basis to determine the level of effectiveness of the advertisements. Likert-scales consist of questions that would be answered by ranking them (Strongly Agree, Agree, Neutral, Disagree, Strongly Disagree)The method used would have been more effective if partnered with a select interview coming from each type of age group. The questionnaire method was proven effective in getting the opinions of the majority of the population. On th e other hand, the interview method could have gotten more in-depth insights or feedback from the consumers regarding their opinion on Coca-Colas advertising and how it affects them as a consumer.4.4 Propose recommendations base on the findings which identify and justify areas for future researchThrough the years, Coca-Cola had always come out strong in their advertising stuffs. Good examples of it would be black eyes Its the Real Thing and Id Like to Buy the World a Coke during the 70s and 80s. These advertisements have helped propel Coca-Cola into its status now as the number one beverage company in the world. However for this decade, Coca-Colas Open Happiness case didnt come out as strong as their previous advertisements. They havent been as visible to the public eye as before. As shown in the first question, a majority of the respondents havent even seen the advertising material of open happiness before.This research has also helped prove that the advertising campaign of Coca -Cola now was rated just above average by the consumers. However, since Coca-Cola has managed to build up loyal consumers through the years, the statistics show that even though the advertising material may come out confusing or just okay, consumers will still continue to patronize Coca-Cola no matter what advertising material they produce. In spite of this, Coca-Cola should not be complacent with their current loyal customers. They should still invest in advertising campaigns that would appeal to their market. They should focus more on the younger generations as they are the group that is still trying to discover new products. Coca-Cola should be able to capture their loyalty for them to be able to stick up their position as the number one beverage in the world.ReferencesQuestionnaires. (n.d.). Retrieved 2012 30-March from Lets Evaluation Resources http//www.shef.ac.uk/lets/evaluate/general/methods-collection/questionnaireWhy+use+questionnaires%3F Data Collection Methods. (n.d.). Retrieved 2012 30-March from Fao Corporate text file Repository http//www.fao.org/DOCREP/003/X2465E/x2465e09.htmb8-6.3.3%20Interviews Primary and Secondary research. (n.d.). Retrieved 2012 2-April from Design and Technology http//hsc.csu.edu.au/design_technology/producing/develop/2662/primary.htm

Mitosis Write-Up

Mitosis (onion inceptions) Root mobile phones are good for observing mitosis this is because theyre in the tip of the root which is an area of the plant that grows quickly. This results in to a greater extent cells going through mitosis all at once, too allowing us to examine the different stages of mitosis. Stages1. Interphase DNA replicates, but has not formed the condensed structure. They remain as loosely coiled chromatin. The nucleus is still intact.2. Prophase The DNA molecules progressively shorten and condense by coiling, to form chromosomes. The stiletto heel fibres are pulled to opposite sides/poles of the cell.3. Metaphase The spindle fibres usurp themselves to the centromeres of the chromosomes.4. Anaphase The spindle fibres shorten and the centromere splits, separated sister chromatids are pulled along behind the centromeres.5. Telophase The chromosomes reach the poles of their respective spindles. Nuclear envelope reform before the chromosomes uncoil. The spindle f ibres disintegrate.Method/Procedure1. Place some premixed 1 molar Hydrochloric acid and Acetic Orcein in the watch glass.Similar essay Why Would We Choose An Embryonic MassBe careful not to get this mixture on your skin or clothing. * Hydrochloric acid (HCL) breaks down the middle lamella and softens the cells tissue and the cell will lose its three-D shape.2. In to this mixture place the terminal (end) 3 or 4 mm of a garlic root (remove the rest of the root). * The cut end postulate to be removed in baseball club to avoid random phantasms.3. Place on the 40oC heating blocks to warm. In a short time (a a couple of(prenominal) minutes) the root tip will feel soft when touched with a mounted needle (Do not let it dry out completely). Heat it in order to speed up the process of the cell wall breaking down, and also for the stain to spread quicker. The stain will bind with the DNA, and it will become more visible.4. Now, using forceps or the mounted needle, pick up the softened roo t tip and transfer it in to a clean drop away.5. Add a few drops of Acetic Orcein6. victimization a mounted needle macerate (Squash) the root tip.7. Once this procedure is complete, apply a clean cover slip to the slide and heat it gently on the 40oC heating blocks for 10 seconds to intensify the stain.This will spread the stain and allow it to bind with the DNA.8. Then invert the slide on a blotting paper and push down ward firmly, applying pressure with your thumb over the cover glass. This should flatten the cells and disperse them so they can be notice under the microscope.This will help flatten it to cell thick.Depending upon how effective your squash has been you may either use this or a pre-prepared slide to observe the stages of mitosis in the root tip you will use either one to identify and record the different stages of mitosis.Variables Independent Variables The slide itself, however, we dont know anything closely the slide.Dependent Variable The percentage of cells in each stage of mitosis. Controlled Variables No. of cells counted. The magnification power used. Were my results valid and reliable? Valid To ensure my results were valid, I compared my results with the other classes results, who were also undertaking the same experiment. Also, I compared them to other results Ive have online, and made sure they both agree. Reliability My results were reliable because, 20 other different students in my class also did the experiment, and my results are the average of them all.Errors I have identified some systematical errors, such as students consistently looking at the wrong voice of the root, as opposed to the growing section. We do not want this as it will damage our resultsHowever, if one individual does this then it will become a random error along with students confusing stages together. e. g. If you look at the attached data student TW overestimated the telophase cells, and underestimated the prophase cells. This is a prime example of a rando m error in my results. Trends and patterns I have identified several trends and patterns in my results, for example the interphase stage took the longest.I expected this to be the case because interphase has along of stage within itself, so it is understandable for it to take considerable more time than the rest. Also, I have noticed that anaphase took the shortest amount of time, as it is just the centromeres splitting and separating. Process of Mitosis If a meeting of cells is dividing rapidly, a high proportion of the cells will be undergoing mitosis. A group of cells that is not dividing will have all cells in interphase of the cell cycle. The amount of cell division occurring in a tissue can be quantified using the mitotic index.The mitotic index is used for studying tumour growth in cancer patients. Using the formula below, calculate the mitotic index for your root tip preparation. If you have time, compare this value with the mitotic index of an area of cells away from the r oot tip and comment on your findings. e. g. Mitotic Index = number of cells containing visible chromosomes total number of cells in the field of view Data analysis DIV/0 = Mean. // DIV0 Of the phases 13. 126315. Precision To the nearest cell (1dp) backing % of time spent in each phase cycle.

Phylogenetic

molecular phyletics An introduction to computational manners and tools for analyzing evolutionary relationships K arn Dowell Math 500 F altogether 2008 molecular(a) Phylogenetics K arn Dowell 1 Abstract molecular phyletics applies a combination of molecular and statistical techniques to infer evolutionary relationships among organisms or genes.This apprizevass account provides a global introduction to phyletics and phyletic shoe points, describes whatever of the about common computational systems use to infer phyletic information from molecular info, and provides an overview of some of the many variant online tools on hand(predicate) for phylogenetic synopsis. In addition, several phylogenetic case studies be summarized to illustrate how re anticipateers in different biological disciplines ar applying molecular phylogenetics in their work. Introduction to molecular(a) PhylogeneticsThe correspondingity of biological melts and molecular mechanisms in quick o rganisms strongly suggests that species descended from a common ancestor. molecular phylogenetics uses the structure and function of molecules and how they diversify over time to infer these evolutionary relationships. This branch of study emerged in the early 20th century plainly didnt begin in earnest until the 1960s, with the advent of protein sequencing, PCR, electrophoresis, and former(a) molecular biology techniques.Over the past 30 years, as computers earn fuck off much powerful and to a greater extent gener completelyy gravelible, and computer algorithmic computer programmes much sophisticated, researchers have been able to tackle the vastly complicated stochastic and probabilistic problems that define evolution at the molecular level to a greater extent effectively. indoors past decade, this field has been further reenergized and re be as whole genome sequencing for intricate organisms has become faster and less expensive. As mounds of genomic data becomes public tot tout ensembleyy available, molecular phylogenetics is continuing to grow and find upstart applications. 4, 10, 17, 20, 22 The primary objective of molecular phylogenetic studies is to recover the dedicate of evolutionary events and represent them in evolutionary steers that graphically depict relationships among species or genes over time. This is an extremely complex unconscious process, further complicated by the fact that there is no champion right way to approach all phylogenetic problems. Phylogenetic data set ups preserve consist of hundreds of different species, each of which may have varying mutation rate and patterns that influence evolutionary change.Consequently, there argon numerous different evolutionary casts and stochastic regularitys available. The optimal methods for a phylogenetic analysis depend on the record of the study and data used. 5, 19, 20 Molecular Evolution Beyond Darwin Evolution is a process by which the traits of a population cha nge from nonp atomic number 18il generation to an other. In On the Origin of Species by convey of Natural Selection, Darwin proposed that, given overwhelming evidence from his extensive relative analysis of living specimens and fossils, all living organisms descended from a common ancestor.The books only illustration (see imagine 1) is a tree diagram diagram-like structure that suggests how tedious and successive modifications could lead to the extreme variations seen in species today. 11, 27 Molecular Phylogenetics Karen Dowell 2 Figure 1. Evolution Defined Graphically. The mend illustration in Darwins Origin of the Species uses a tree-like structure to describe evolution. This drawing shows ancestors at the limbs and branches of the tree, more(prenominal) recent ancestors at its twigs, and contemporary organisms at its buds. 34 Darwins surmise of evolution is found on tether underlying principles ariation in traits exist among individuals within a population, these varia tions piece of tail be passed from one generation to the conterminous via inheritance, and that some forms of inherited traits provide individuals a higher chance of survival and reproduction than others. 11 Although Darwin developed his theory of evolution without any knowledge of the molecular basis of behavior, it has since been crackd that evolution is actually a molecular process based on genetic information, encoded in desoxyribonucleic social disease, RNA, and proteins. At a molecular level, evolution is operate by the same hookeds of mechanisms Darwin observed at the species level.One molecule undergoes diversification into many variations. One or more of those variants brook be selected to be reproduced or amplified throughout a population over many generations. much(prenominal) variations at the molecular level can be caused by mutations, such as deletions, insertions, inversions, or substitutions at the al-Qaida level, which in turn affect protein structure a nd biological function. 11, 22 What is a organic evolution? According to youthful evolutionary theory, all organisms on earth have descended from a common ancestor, which means that any set of species, extant or extinct, is related.This relationship is called a organic evolution, and is represented by phylogenetic trees, which graphically represent the evolutionary history related to the species of interest (see Figure 2). Phylogenetics infers trees from observations about existing organisms victimisation morphological, physiological, and molecular characteristics. Figure 2. Phylogeny of Mammalia. This phylogenetic tree shows the evolutionary relationships among six orders of Mammalian species (taxa). Taxa listed in grey are extinct. The tree of life represents a phylogeny of all organisms, living and extinct.Other, more specialized species and molecular phylogenies are used to sign comparative studies, test biogeographic hypotheses, evaluate mode and timing of speciation, inf er aminic acid chronological succession of extinct proteins, track the evolution of diseases, and even provide evidence in criminal cases. 19 Molecular Phylogenetics Karen Dowell 3 Understanding Phylogenetic Trees Before exploring statistical and bioinformatic methods for estimating phylogenetic trees from molecular data, its important to have a basic familiarity of the terms and elements common to these types of trees. See Figure 3. ) Figure 3. Basic elements of a phylogenetic tree. Phylogenetic trees are composed of branches, also known as edges, that connect and terminate at nodes. Branches and nodes can be internal or external (terminal). The terminal nodes at the tips of trees represent operational systematic units (OTUs). OTUs gibe to the molecular seasons or taxa (species) from which the tree was inferred. Internal nodes represent the last common ancestor (LCA) to all nodes that muster from that point.Trees can be made of a single gene from many taxa (a species tree) or multi-gene families (gene trees). 1, 10 A tree is considered to be rooted if there is a particular node or outgroup (an external point of reference) from which all OTUs in the tree arises. The root is the oldest point in the tree and the common ancestor of all taxa in the analysis. In the absence of a known outgroup, the root can be placed in the middle of the tree or a rootless tree may be sustaind. Branches of a tree can be grouped together in different ways. (See Figure 4. ) Figure 4. multitudes and associations of taxonomical units in trees. A monophyletic group consists of an internal LCA node and all OTUs arising from it. All members within the group are derived from a common ancestor and have inherited a set of unique common traits. A paraphyletic group excludes some of its descendents (for examples all mammals, except the marsupialia Molecular Phylogenetics Karen Dowell 4 taxa). And a polyphyletic group can be a army of distantly related OTUs that are associated by a simi lar characteristic or phenotype, but are not directly descended from a common ancestor. 1, 17 Trees and Homology Evolution is do by homology, which refers to any similarity due to common ancestry. Similarly, phylogenetic trees are outlined by homologous relationships. Paralogs are homologous places separate by a gene duplication event. Orthologs are homologous sequences separated by a speciation event (when one species diverges into dickens). Homologs can be either paralogs or orthologs. 1, 11, 22 Molecular phylogenetic trees are drawn so that branch distance corresponds to amount of evolution (the part difference in molecular sequences) between nodes. 1, 19 Figure 5. Understanding paralogs and orthologs. Paralogs are created by gene duplication events. (See Figure 5. ) once a gene has been duplicated, all subsequent species in the phylogeny leave behind inherit both(prenominal)(prenominal) copies of the gene, creating orthologs. Interestingly, evolutionary divergence of d ifferent species may get out in many variations of a protein, all with similar structures and functions, but with very different amino acid sequences. Phylogenetic studies can trace the origin of such proteins to an transmittable protein family or gene. 1, 22 Figure 6. Mirror Phylogenies. component A and Gene A1 are paralogs, whereas all instances of Gene A are orthologs of each other in different Canid species. One way to ensure that paralogs and orthologs are suitably referenced in a phylogenetic tree, and guard against mis design due to missing or broken taxonomic information is to generate mirror phylogenies (see Figure 6) in which paralogs serve as each others outgroup. 1, 4, 19, 22 Estimating Molecular Phylogenetic Trees Molecular phylogenetic trees are generated from character datasets that provides evolutionary guinea pig and context.Character data may consist of biomolecular sequence fusions of DNA, RNA, or amino acids, molecular markers, such as single stand polymor phisms (SNPs) or restriction fragment length polymorphisms (RFLPs), morphology data, or information on gene order and content. Evolution is modeled as a process that changes the state of a character, such as the type of root word (AGTC) at a Molecular Phylogenetics Karen Dowell 5 specific location in a DNA sequence each character is a function that maps a set of taxa to distinct states. 1, 19 Note that roughly of the examples in this paper use DNA sequences as character data, but trees can be accurately estimated from many different types of molecular data. Figure 7. Evolution of a DNA Sequence Figure 7 illustrates how a molecular sequence might evolve over time as a result of multiple mutations that results small, but evolutionarily important changes in a nucleotide sequence. At the protein level, these changes may not initially affect protein structure or function, but over time, they may eventually shape a new purpose for a protein within divergent species. 10, 19, 22 OTUs can be used to hold an unrooted phylogenetic tree that clearly depicts a path of evolutionary change. Steps in Phylogenetic abbreviation Although the nature and scope of phylogenetic studies may vary importantly and command different datasets and computational methods, the basic step in any phylogenetic analysis remain the same assemble and align a dataset, build (estimate) phylogenetic trees from sequences using computational methods and stochastic models, and statistically test and assess the estimated trees. 4, 19, 20 Assemble and Align Datasets The firstborn step is to strike a protein or DNA sequence of interest and assemble a dataset consisting of other related sequences. For example, to explore relationships among different members of the Notch family of proteins, one might select DNA sequences for Notch1 through Notch4, in different species, such as human, dog, rat, and mouse, then perform a multiple sequence alignment to identify homologies. 1, 10, 13, 19, 20 There are a number of free, online tools available to simplify and streamline this process. DNA sequences of interest can be retrieved using NCBI BLAST or similar search tools.When evaluating a set of related sequences retrieved in a BLAST search, pay close attention to the score and E-value. A high score indicates the subject sequence retrieved with closely related to the sequence used to initiate the query. The smaller the E-value, the higher the hazard that the homology reflects a true evolutionary relationship, as opposed to sequence similarity due to chance. As a general rule, sequences with E-values less than 10-5 are homologs of a query sequence. 10 Once sequences are selected and retrieved, multiple sequence alignment is created.This involves musical arrangement a set of sequences in a matrix to identify regions of homology. Typically, gaps (one or more spaces in the alignment) are introduced in one or more sequences to represent insertions or deletions in the molecular code that may have occurred over time. Effective multiple sequence alignment hinged on gap analysis find out where to insert gaps and how large to make them. There are many websites and software programs, such as ClustalW, MSA, MAFFT, and T-Coffee, designed to perform multiple sequence on a given set of molecular data. ClustalW is currently the around mature and most widely used. 1, 10. 19 Molecular Phylogenetics Karen Dowell 6 Building Phylogenetic Trees To build phylogenetic trees, statistical methods are applied to determine the tree network topology and calculate the branch lengths that best describe the phylogenetic relationships of the aligned sequences in a dataset. Many different methods for building trees exist and no single method performs well for all types of trees and datasets. The most common computational methods applied acknowledge aloofness-matrix methods, and clear-cut data methods, such as supreme parsimony and level best likeliness. 4, 17, 20 There are several software packages, such as Paup*, PAML, PHYLIP, that apply most popular methods. 4 Paup* is a commercially available program that implements a wide signifier of methods for phylogenetic inference, including maximum likelihood analysis for DNA data using different models. Paup* also includes a set of exact and heuristic methods for searching optimal trees. PAML (Phylogenetic Analysis by Maximum Likelihood) is open-access set of programs for phylogenetic analysis and evolutionary model comparison.PAML includes many advanced modelsDNA- and AAbased models as well as codon-based models that can be used to detect positive selection. Many of the programs in PAML can model heterogeneity of evolutionary rates among sequence sites using ? distributions, and evolutionary dynamics of different sequence regions (concatenated gene sequences). PHYLIP is another large suite of open-access programs for phylogenetic inference that estimates trees using numerous methods, including pairwise distance, maximum parsimony, and maximum likelihood.The maximum likelihood programs can traverse a a few(prenominal) simple stochastic models and have equitable tree searching capabilities. PHYLIP is generally considered good educational software for novice phylogeneticists. Distance-Matrix Methods Distance matrix methods compute a matrix of pairwise distances between sequences that boisterous evolutionary distance. Distance-based methods tend to be in polynomial time and are quite fast in practice. These methods use thuding techniques to compute evolutionary distances, such as the number of nucleotide or amino acid substitutions between sequences, for all pairs of taxa.They then construct phylogenetic trees using algorithms based on operational relationships among distance values. There are several different distance-matrix methods, including the Unweighted Pair-Group Method with Arithmetic Mean (UPGMA), which uses a back-to-back clustering algorithm the Transformed Distance Method, which us es an outgroup as a reference, then applies UPGMA the Neighbor-Relations Method, which applies 4point condition to adjust the distance matrix, then applies UPGMA and the Neighbor-Joining Method, which arranges OTUs in a star, the finds neighbors sequentially to minimize total length of tree. 4, 17 The following naval division on the UPGMA method provides a more detailed example of how distance-matrix methods work. UPGMA Method UPGMA produces rooted trees for which the edge lengths can be viewed as times measured by a molecular clock with a ageless rate. This method uses a sequential clustering algorithm to identify two OTUs that are most similar (meaning they have the shortest evolutionary distance and are most similar in sequence) and treat them as a single new composite OTU. This process is restate iteratively until only two OTUs remain.The algorithm defines the distance (d) between two clusters Ci and Cj as the average distance between pairs of sequences from each cluster Mole cular Phylogenetics Karen Dowell 7 Where Ci and Cj are the number of sequences in clusters i and j. This sequential clustering process is visually described in Figure 8. In this example, the two most homologous sequences are 1 and 2. They are clustered into a new composite parent node (6), and the branch lengths (t1 and t2) are defined as 1/2d1,2. The next step is to search for the closest pair among remaining sequences and node 6.Pair 4 and 5 are identified and clustered into a new parent node (7), and the branch length for t4 and t5 is calculated. 4, 17 Figure 8. Sequential clustering of sequences using the UPGMA method. 17 In this interactive process, parent node 8 is created from pairs 7 and 3, and parent node 9 is created by clustering nodes 6 and 8. 4, 17 Thus, all sequences are clustered into a single evolutionary tree. The total time (t9) can be calculated as D6,8 = 1/6 (d1,3 + d1,4 + d1,5 + d2,3 + d2,4 +d2,5)Discrete Data Methods Discrete data methods examine each editoria l of a multiple sequence alignment dataset separately and search for the tree that best represents all this information. Although distance-based methods tend to be much faster than discrete data methods, they typically yield little information beyond the basic tree structure. Discrete data analyses, on the other hand, are information rich. These methods produce a separate tree for each column in the alignment, so it is possible to trace the evolution for specific elements within a given sequence, such as catalytic sites or regulatory regions. 10, 17, 19, 20) Commonly used discrete data methods include maximum parsimony, which searches for the most parsimonious tree that overlooks the least number of evolutionary changes to explain differences observed, maximum likelihood, which requires a probabilistic model for the process of nucleotide substitution, and Bayesian MCMC, which also requires a stochastic model of evolution, but creates a probability distribution on a set of trees or aspects of evolutionary history. 17, 19, 20 Discrete data methods are generally considered to produce the best estimates of evolutionary history.However, these methods can be computationally expensive, and it can take weeks or months to mystify a reasonable level of accuracy for moderate to large datasets with 100 or more OTUs. 19 Molecular Phylogenetics Maximum Parsimony Karen Dowell 8 Among the most widely used tree-estimation techniques, maximum parsimony applies a set of algorithms to search for the tree that requires the minimum number of evolutionary changes observed among the OTUs in the study. For example, Figure 9 lists four sample sequences from which phylogenetic trees could be inferred using maximum parsimony. come out Seq 1 2 3 4 1 A A A A 2 A G G G 3 G C A A 4 A C T G 5 G G A A 6 T T T T 7 G G C C 8 C C C C 9 A G A G Figure 9. standard sequences for a maximum parsimony study 17 Maximum parsimony algorithms identify phylogenetically informative sites, meaning the site favors some trees over others. Consider the sequences in Figure 9 billet 1 is not informative, because all sequences at that site (in column 1) are A (Adenine), and no change in state is required to yoke any one sequence (1-4) to another.Similarly, internet site 2 is not informative because all three trees require one change and there is no reason to favor one tree over another. Site 3 is not informative because all three trees require two changes. (See Figure 10). Figure 10. Site 3 trees all require one evolutionary change. 17 Site 4 is not informative because all three trees require three changes. No one tree can be identified as parsimonious. (See Figure 10 Figure 11. Site 4 trees all require three evolutionary changes. 17 Site 5 is informative because one tree requires only one nucleotide change, whereas the other two trees require 2 changes.In Figure 12, the first tree on the left, which requires only one nucleotide change, is identified as the maximum parsimony tree. Figur e 12. Site 5 trees vary in the number of evolutionary changes required. 17 Molecular Phylogenetics Maximum Likelihood Karen Dowell 9 The maximum likelihood method requires a probabalistic model of evolution for estimating nucleotide substitution. This method evaluates competing hypotheses (trees and parameters) by selecting those with the highest likelihood, meaning those that render the observed data most plausible. The ikelihood of a hypothesis is defined as the probability of the data given that hypothesis. In phylogeny reconstruction, the hypotheses are the evolutionary tree (its topology and branch lengths) and any other parameters of the evolutionary model. 17, 20 The likelihood calculations required for evolutionary trees are far from straightforward and usually require complex computations that must allow for all possible unobserved sequences at the LCA nodes of hypothesized trees. This method specifies the spiritual rebirth probability from one nucleotide state to another in a time interval in each branch.For example, for a one-parameter model with rate of substitution ? per site per unit time, the probability that the nucleotide at time t is i is The probability that the nucleotide at time t is j is To set up a likelihood function, given x as the transmitted node and y and z as internal nodes, the probability of observing nucleotides i, j, k, l at the tips of the tree is computed as Pxl(t1+t2+t3)Pxy(t1)Pyk(t2+t3)Pyz(t2)Pzi(t3)Pzj(t3) For the ancestral node (root) x, the probability of having nucleotide l in sequence 4 is calculated as Pxl(t1+t2+t3)Because x, y, and z can be any one of four nucleotides (ACGT), it is necessary to sum over all possibilities to obtain the probability of observing the configuration of nucleotides i, j, k, l, in sequences 1, 2, 3, 4, for a given hypothetical tree (see Figure 13. ). This likelihood probability is calculated as h(I,j,k,l)= ? gxPxl(t1+t2+t3) ? Pxy(t1)Pyk(t2+t3) ? Pyz(t2)Pzi(t3) Pzj(t3) The appropriate li kelihood function depends on the hypothetical tree and the evolutionary model used. (See Figure 13. ) 17 Figure 13. Different types of model trees for the derivation of the maximum likelihood function. 17 Molecular Phylogenetics stochastic Models of Evolution Karen Dowell 10 evolutionary changes in molecular sequences result from mutations, some of which occur by chance, others by natural selection. Rates of change can also differ among OTUs, depending on several factors ranging from GC content to genome size. To accurately estimate phylogenetic trees, assumptions must be made about the substitution process and those assumptions must be stated in the form of a stochastic evolutionary model. These probabilistic models are used to rank trees according to likelihood P(datatree).From a Bayesian perspective, they rank trees according to a posterior probability P(treedata). 17, 20 The objective of probabilistic models is to find likelihood or posterior probability of a particular taxonomi c feature, then define and compute P(x? T,t ? ) Where x ? is xj for j=1n, T is a tree with n leaves with sequence j at leaf j, and t ? are tree edge lengths. 17 A few popular stochastic models of evolution include the single parameter Jukes-Cantor (JC) method, Kimura 2-parameter (K2P), Hasegawa-Kishino-Yano (HKY), and Equal-Input.Some software programs, such as Paup*, will mechanically use a default model for the tree estimation method chosen. The JC method is the easiest one to comprehend, because it assumes that if a site changes its state, it changes with equal probability to the other states. This is not very realistic, however, as some sites are known to evolve more rapidly than others, and some sites may be invariable and not allowed to change at all. Determining how best to select the appropriate model is a topic of another paper (or papers) as there is no one model that incorporates all mutation rules and patterns across different species and macromolecules. 4, 17, 20 dark Markov Models Profile hidden Markov models (HMMs) are a form of Bayesian network that provides statistical models of the consensus structure of a sequence family. Gary Churchill at The Jackson Lab was the first evolutionary geneticist to propose using profile HMMs to model rates of evolution. Many software packages and web services now apply HMMs to estimate phylogenetic relationships. 8 In the HMM format, each position in the model corresponds to a site in the sequence alignment. For each position, there are a number of possible states, each of which corresponds to a different rate of evolution.In addition, transitions between all possible rate-states at adjacent positions. Transition probabilities suppress any tendency for patterns of rates to occur in successive sites. 2, 4 Assessing Trees Tree estimating algorithms generate one or more optimal trees. This set of possible trees is subjected to a series of statistical tests to evaluate whether one tree is better than another and if the proposed phylogeny is reasonable. Common methods for assessing trees include the Bootstrap and Jackknife Resampling methods, and analytical methods, such as parsimony, distance, and likelihood.To illustrate how these methods are used, consider the steps conglomerate in a bootstrap analysis. Bootstrap Analysis A bootstrap is a statistical method for assessing trees that takes its name from the fact that it can pull itself up by its bootstraps and generate meaningful statistical distributions from about nothing. Using bootstrap analysis, distributions that would otherwise be difficult to calculate exactly are estimated by repeated creation and analysis of artificial datasets. In a Non-parametric bootstrap, artificial datasets Molecular Phylogenetics Karen Dowell 11 generated by resampling from cowcatcher data.In a parametric bootstrap, data is simulated according to hypothesis tested. The objective of any bootstrap analysis is to test whether the whole dataset supports the tree. 1, 4, 17 Figure 14 illustrates the basic steps in any bootstrap analysis. Sample datasets are mechanically generated from an original dataset. Trees are then estimated from each sample dataset. The results are compiled and comparabilityd to determine a bootstrap consensus tree. Figure 14. Steps in a phylogenetic tree bootstrap analysis. 1 Phylogenetic Analysis Tools There are several good online tools and databases that can be used for phylogenetic analysis.These include PANTHER, P-Pod, PFam, TreeFam, and the PhyloFacts geomorphologic phylogenomic encyclopedia. Each of these databases uses different algorithms and draws on different sources for sequence information, and therefore the trees estimated by PANTHER, for example, may differ significantly from those generated by P-Pod or PFam. As with all bioinformatics tools of this type, it is important to test different methods, compare the results, then determine which database works best (according to consensus results, not res earcher bias) for studies involving different types of datasets.In addition, to the phylogenetic programs already mentioned in this paper, a universal list of more than 350 software packages, web-services, and other resources can be tack together here http//evolution. genetics. washington. edu/phylip/software. html. PANTHER (pantherdb. org) Protein outline Through evolutionary Relationships, known by its acronym PANTHER, is a library of protein families and subfamilies indexed by function. Panther version 6. 1 contains 5547 protein families. Molecular Phylogenetics Karen Dowell 12It categorizes proteins by evolutionary related proteins (families) and related proteins with same function (subfamilies). 8, 21, 26 PANTHER is composed of both a library and index. The library is a collection of books that represent a protein family as a collection of multiple sequence alignments, HMMs, and a family phylogenetic tree. Functional divergence within the tree is represented by dividing the p arent tree into child trees and HMMs based on shared functions. These subfamilies enable database curators to more accurately capture operable divergence of protein sequences as inferred from genomic DNA. 25, 26 PANTHER database entries are annotated to molecular function, biological process and pathway with a proprietary PANTHER/X ontology system, which is supposed to be easier to understand than the more global standard Gene Ontology (GO). Database entries in PANTHER are generated through clustering of UniProt database using a BLAST-based similarity score. Trees are automatically generated based on multiple sequence alignments and parameters of the protein family HMMs using the Tree Inferred from Profile Score (TIPS) clustering algorithm.Scientific curators review all family trees, annotate each tree, and determine how best to divide them into subtrees using a tree-attribute viewer that tabulates annotations for sequences in a tree. In addition, trees and subfamilies are manually cross-checked and validated by curators. 25, 26 P-POD (ortholog. princeton. edu) The Princeton Protein Orthology Database (P-POD) combines results from multiple comparative methods with curated information culled from the literature.Designed to be a resource for experimental biologists seeking evolutionary information on genes on interest, P-POD employs a standard architecture, based on their Generic Model Organism Database (GMOD). P-POD can be accessed from their web service or downloaded to result on topical anaesthetic computer systems. 12 P-POD accepts FASTA-formatted protein sequences as input, and performs comparative genomic analyses on those sequences using OrthoMCL and Jaccard clustering methods. The P-POD database contains both phylogenetic information and manually curated experimental results.The site also provides many links to sites rich in human disease and gene information. This tool may be particularly utile for bioinformaticists and statisticians developing com parative genomic database tools and resources. Pfam (pfam. sanger. ac. uk/) PFam is a collection of protein families represented by multiple sequence alignments and HMMs. It contains models of protein clans, families, domains, and motifs, and uses HMMs representing conserved running(a) and geomorphologic domains. It is a large, widely used, actively curated mature database that has been available online since 1995.Pfam can be used to retrieve the domain architectures for a specific protein by conducting a search using a protein sequence against the Pfam library of HMMs. This database is also helpful for proteomes and protein domain architecture analysis. 6, 8, 24 There are two versions of the Pfam database PfamB is generated automatically from ProDom, using PsiBLAST, an open access bioinformatics tool available through NCBI for identifying weak, but biologically relevant sequence similarities. Pfam-A is hand-curated from custom multiple sequence alignments. Pfam protein domain fami lies are clustered with Mkdom2, and aligned with ProDomAlign.ProDom is a comprehensive set of protein domain families automatically generated from the SWISSPROT and TrEMBL sequence databases. Mkdom2 is a ProDom program used to make ProDom family clusters. Protein domain families in ProDom were aligned using an improved parallelized program called Molecular Phylogenetics Karen Dowell 13 ProDomAlign, developed in C++ using OpenMP. ProDomAlign is based on MultAlign, a program well suited for aligning very large sequence families with thousands of associated sequences. As of early 2008, Pfam matched 72 percent of known proteins sequences, and 95 percent of proteins for which there is a known structure.Within the Pfam database, 75 percent of sequences will have one match to Pfam-A, 19 percent to Pfam-B. There are also two versions of Pfam-A and Pfam-B. Pfam-ls handles global alignments, and Pfam-fs is optimized for local alignments. Interestingly, Pfam entries can be classified ad as unk nown, but that doesnt mean the protein is undocumented. Unknown entries can be proteins for which some information is known, but it has not been fully researched or cannot be adequately annotated. For example, Pfam entry PFO1816 is a LeucineRich Repeat Variant (LRV), which has a known structure (1LRV) available in the Protein Databank (pdb. rg). LRV repeat regions, which are found in many different proteins, are often involved in cell adhesion, DNA repair, and endocrine receptionbut identification of an LRV within a sequence encoding a protein doesnt specifically reveal the proteins function. For studies involving a large number of protein searches, it may be more convenient to run Pfam locally on a client machine. The standalone Pfam system requires the HMMER2 software, the Pfam HMM libraries and a couple of additional files from the Pfam website to be installed on the client machine. HMMER is a freely distributable implementation of profile HMM software for protein sequence analy sis. ) Once the initial search is complete, researchers can go to the Pfam website to further analyze select number of sequences using additional features on website. 6, 8, 24 TreeFam (TreeFam. org) TreeFam is a curated database of phylogenetic trees and orthology fortune tellings for all animal gene families that focuses on gene sets from animals with completely sequenced genomes. Orthologs and paralogs are inferred from phylogenetic tree of gene family.Release 4 contains curated trees for 1314 families and automatically generated trees for another 14351 families. 16, 23 Like Pfam, TreeFam is a two-part database TreeFam-B contains automatically generated trees, and TreeFam-A consists of manually curated trees. To automatically generate trees, an algorithm selects clusters of genes to create TreeFam-B generators from core species with high-quality reference genome sequences, first using BLAST to rapidly assemble an initial list of possible matches, then HMMER to expand and filter probable sequence matches for each TreeFam B seed family.The filtered alignment is fed into a neighbor-joining algorithm and a tree is constructed based on amino acid mismatch distances. For TreeFam version 4, the most current release, five clean family trees were built for each TreeFam B seed, two using a maximum likelihood tree generated using PHYML (one based on the protein alignment, the other on codon alignment), three using a neighbor joining tree, using different distance measurements based on codon alignments. 16, 23 Scientific curators then manually any correct errors (based on information in the literature) in automatically generated TreeFam-B trees. Curated TreeFam-B trees then become seeds for TreeFam-A trees. Clean TreeFam-A trees are build using three merging algorithms and bootstrapping to find the consensus tree of seven trees two constrained maximum likelihood trees based on protein and codon alignment, and five unconstrained neighbor-joining trees generated using d ifferent distance measurements based on codon alignments.For both TreeFam-B and TreeFam-A families, orthologs and paralogs are inferred only from clean trees using extra/Loss Inference (DLI) algorithm that requires a species tree (NCBI taxonomy tree). 16, 23 Molecular Phylogenetics PhyloFacts (phylogenomics. berkeley. edu/phylofacts) Karen Dowell 14 PhyloFacts is an online phylogenomic encyclopedia for protein functional and morphological classification. It contains more than 57,000 books for protein superfamilies and structural domains.Each book contains heterogenous data for protein families, including multiple sequence alignments, one or more phylogenetic trees, predicted 3-D protein structures, predicted functional subfamilies, taxonomic distributions, GO annotations, and PFAM domains. HMMs constructed for each family and subfamily permit novel sequences to be classified to different functional classes. 14 Unlike other databases mentioned in this paper, PhyloFacts seeks to cor rect and clarify annotation errors associated with computational methods for predicting protein function based on sequence homology.It uses a consensus approach that integrates many different prediction methods and sources of experimental data over an evolutionary tree. By applying evolutionary and structural clustering of proteins, PhyloFacts is able to analyze disparate datasets using multiple methods, identify potential errors in database annotations, and provide a mechanism for improving the accuracy of functional annotation in general. 14 PhyloFacts can be used to search for protein structure prediction or functional classification for a particular protein sequence.Researchers may also browse through protein family books and multiple sequence alignments, phylogenetic trees, HMMs and other pertinent information for proteins of interest. This webservice also provides many links to literature and other information sources. 14 apply Molecular Phylogenetics Molecular phylogenetic s tudies have many diverse applications. As the amount of publically available molecular sequence data grows and methods for modeling evolution become more sophisticated and accessible, more and more biologists are incorporating phylogenetic analyses into their research trategy. Heres a sampling of how molecular phylogenetics might be applied. Tracing the evolution of man In one case study, molecular phylogenetic techniques were used to compare and analyze variation in DNA sequences using modern-day human and Neanderthal mitochondrial DNA (mtDNA). For this study, 206 modern human mtDNAs and parts of two Neanderthal mtDNAs sequences derived from skeletal remains were used to generate an initial dataset. heritable distance was first estimated using the Jukes-Cantor single parameter model.Then the Kimura 2-Parameter model was used to distinguish between transition (replacement of one purine with another purine or one pyrimidine with another pyrimidine) and transversion (replacement of one purine with a pyrimidine or vice versa) probabilities with Kimura 2parameter model. A phylogenetic tree representing primate evolution was generated using pairwise genetic distances between primate Hypervariable regions I and II of mtDNA. 3 Chasing an plaguey SARS Using publically available genomic data, it is possible to reconstruct the progression of the SARS epidemic over time and geographically.To conduct this phylogenetic analysis, researchers used the neighborjoining method to construct a phylogenetic tree of spike proteins in various coronaviruses and identify the viral host (a Himalyan palm civet). They then obtained 13 severe acute respiratory syndrome genome sequences with documented information on the date and location of the sample. The neighbor-joining method and a distance matrix based on Jukes-Cantor model, were used to generate an epidemic tree, from which it was possible to identify the origin (date and location) of the virus by observing progression of mutatio ns over time. 3 Molecular Phylogenetics Barking up the right tree Karen Dowell 15 Phylogenetics is increasingly incorporated into biological and biomedical research papers. When the canine genome was published, researchers used sequence data to estimate a comprehensive phylogeny of the canid family. Figure 15. Phylogenetic Tree of the Canid family This canid family phylogenetic tree is based on 15 kb of exon and intron sequence. It was constructed using the maximum parsimony method and represents the single most parsimonious tree.A good example of how phylogenies are referenced in the literature, this tree includes bootstrap values and Bayesian posterior probability values listed above and below internodes, respectively. Dashes indicate bootstrap values below 50%. In addition, divergence time in millions of years (Myr) is indicated for three nodes. 18 Seeing the Forest from the Trees Molecular phylogenetics is a broad, diverse field with many applications, supported by multiple comp utational and statistical methods. The sheer volumes of genomic data currently available (and rapidly growing) render molecular phylogenetics a key component of much biological research.Genome-scale studies on gene content, conserved gene order, gene expression, regulatory networks, metabolic pathways, functional genome annotation can all be enriched by evolutionary studies based on phylogenetic statistical analyses. 19, 25 27 Molecular phylogenies have fast become an integral part of biological research, pharmaceutical drug design, and bioinformatics techniques for protein structure prediction and multiple sequence alignment. Although not all molecular biologists and bioinformaticians may be familiar with the techniques describedMolecular Phylogenetics Karen Dowell 16 in this paper, this is a rapidly growing and expanding field and there is ongoing need for novel algorithms to solve complex phylogeny reconstruction problems. References 1. Baldauf, SL (2003) Phylogeny for the faint of heart a tutorial. Trends in Genetics, 19(6)345-351. 2. Brown, D, K Sjolander (2006) Functional smorgasbord Using Phylogenomic Inference. PLos Computational Biology, 2(6)0479-0483. 3. Cristianini, N, and M Hahn (2007) Introduction to Computational Genomics A Case Studies Approach.Cambridge University Press Cambridge. 4. Durbin, R, S Eddy, A Krogh, G Mitchison (1998) Biological Sequence Analysis. Cambridge University Press Cambridge. 5. Ewens, WJ, R Grant (2005) Statistical Methods in Bioinformatics. Springer attainment and Business Media New York. 6. 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Thomas, PD, MJ Campbell, A Kejariwal, H Mi, B Karlak, R Daverman, K Diemer, A Muruganujan, A Narechania. PANTHER A Library of Protein Families and Subfamilies Indexed by Function. Genome Research, 132129-2141. 27.Warnow, T (2004) Computational Methods in Phylogenetics Computational Systems Biology Conference, Stanford, CA 28. Whelan, S, P Lio, N Goldman (2001) Molecular phylogenetics state of the art methods for looking into the past. Trends in Genetics, 17(5)262-272. Molecular Phylogenetics Karen Dowell 18 Appendix Website Resources Phylogeny Programs. A University of chapiter site formerly supported by the National Science Foundation. http//www. evolution. g enetics. washington. edu/phylip/software. tml TreeFam Tree Families Database. http//wwww. treefam. org Protein Analysis Through Evolutionary Relationships (PANTHER) Classification System. http//www. pantherdb. org. 29. Pfam Database of Protein Families. http//pfam. sanger. ac. uk 30. Princeton Protein Orthology Database (P-POD). http//ppod. princeton. edu 31. Wikipedia. http//en. wikipedia. org/wiki/Tree_of_life(science) Cover Page The cover image is from a phylogeny of canid species that appeared in Lindblad-Toh et al, 2005. 18