Rosana Fernandes da Cunha

Ensaio opcional - 10/03/17

The central dogma of molecular biology, proposed by Crick in 1958, deals with the transmission of genetic information in biological systems. In this flow of information the same message is encoded from different ways. However, as dogma itself has already emphasized, and several studies of this phenomenon later, once this information has passed into protein, it cannot be further recoded into RNA or DNA again. An amino acid (unit that forms the proteins) can be encoded by more than one codon (triplet of bases). In observing amino acids, it is noted that the nucleotides of the third position of the codon undergo a high mutation rate (mainly because of the conformation of the ribosome in the third base, which facilitates the modification of the last nucleotide of the triplet), and this change may or may not generate a new amino acid in the protein sequence. For example, proline can be encoded by four different codons (CCA, CCC, CCG, CCU), if only the nucleotide of the last position undergoes a mutation, the amino acid will remain proline and there will be no change in the formation of the protein. This process will create a "noise" in genetic analysis. But what these different rates of mutations in the nucleotides of an amino acid can tell us about the dogma? Who performs and undergoes evolutionary pressures are the proteins and what they do. Its genetic sequences are less conserved and susceptible to higher mutation rates, which makes it difficult for a protein to decode the genetic sequence of RNA and/or DNA that gave rise to it, corroborating the premise of dogma that the transfer of information from proteins to RNA or DNA does not exist. From the above, it is concluded that, despite more than 50 years of its formulation, central dogma remains crucial in the interpretation of molecular phenomena and serves as a subsidy for current (and future) works on the transfer of genetic information.

Revisado por: Alfredo de Souza

The central dogma of molecular biology, proposed by Crick in 1958, deals with the transmission of genetic information in biological systems (Não parece ser a ideia central, Topic sentence). In this flow of information (virgula?) the same message is encoded from ("From" -> "in") different ways. However, as (the) dogma itself has already emphasized, and several studies of this phenomenon later, once this information has passed into protein, it cannot be further recoded into RNA or DNA again. An amino acid (unit that forms the proteins) can be encoded by more than one codon (triplet of bases). In (Retirar o "In") observing amino acids, it is noted that the nucleotides of the third position of the codon undergo a high mutation rate (mainly because of the conformation of the ribosome in the third base, which facilitates the modification of the last nucleotide of the triplet), and this change may or may not generate a new amino acid in the protein sequence (Talvez esta seja a ideia da Topic sentence). For example, proline can be encoded by four different codons (CCA, CCC, CCG, CCU), if only the nucleotide of the last position undergoes a mutation, the amino acid will remain proline and there will be no change in the formation of the protein. This process will create a "noise" in genetic analysis. But what these different rates of mutations in the nucleotides of an amino acid can tell us about the dogma? Who performs and undergoes evolutionary pressures are the proteins and what they do. Its genetic sequences are less conserved and susceptible to higher mutation rates, which makes it difficult for a protein to decode the genetic sequence of RNA and/or DNA that gave rise to it, corroborating the premise of dogma that the transfer of information from proteins to RNA or DNA does not exist. From the above, it is concluded that, despite more than 50 years of its formulation, central dogma remains crucial in the interpretation of molecular phenomena and serves as a subsidy for current (and future) works on the transfer of genetic information.

Comentários gerais:
- A ideia central foi bem escolhida. A discussão sobre código degenerado é bastante pertinente e interessante para o tema que estamos trabalhando. A ideia geral passada pelo parágrafo esta bem embasada em conceitos fundamentais da biologia molecular.
- O parágrafo não possui uma Topic sentence. Isso dificultou identificar qual a mensagem central apresentada ou defendida no texto;
- A ideia central aparece no meio do texto e sem muita relação com as frases anteriores. A ideia de discutir o código degenerado apareceu de surpresa, talvez pudesse fazer parte da primeira sentença do parágrafo;
- Algumas frases longas dificultaram a compreensão. Maior números de pontos podem auxiliar nesta questão;
- Os pontos discutidos no desenvolvimento não remetem de forma clara e direta à conclusão. Algumas frases apresentadas no texto não adicionaram informações necessárias para a compreensão da ideia central. Tais informações a mais desviam o foco e diluem o poder dos argumentos centrais.**


Ensaio 1 - 17/03/17

Proofreading is a repair performed by DNA polymerase itself, in this process it detects whether a nucleotide has been added incorrectly, removes it and adds the correct one before continuing DNA synthesis, but not all polymerases have this function. Why does it happen? What would be the advantage of not having a repair tool? It sounds crazy! When we think that many degenerative and lethal mutations cease to be expressed because the repairing machinery, it is even difficult to believe that there are organisms that "prefer" not to have it in their composition. However, they do exist! Some Bacteria and Archaea do not present proofreading in their DNA polymerases. For these organisms, which want to have a gigantic population, maintaining mutation errors can be beneficial. How can this be positive? The number of organisms in these populations is very large, the conservation of high error rates can end up generating a "successes" that, from generation to generation, becomes an evolutionary gain. Due to the large number of individuals in these populations, this process ends up being feasible, since the loss of organisms does not affect their maintenance. The eukaryotic repair machinery, however, is more refined. Because they are smaller populations, they can not afford the "luxury" of losing their organisms, this diminishes the reproductive power and the gene flow among individuals, which can lead them to extinction!

Revisado por: Lyslaine Sato

A ideia to texto foi bem desenvolvida
Os questionamentos ao longo do texto proporcionam uma discussão interessante e uma abordagem informal ao tema, que deve ser adotado com cautela de acordo a finalidade do texto
Poderia ter sido utilizado ponto final ao expor o seu topic sentence.


Ensaio 2 - 24/03/17

The neutral theory proposes that patterns exist without the need of the natural selection, and that 99% of them are caused only by stochastic events. Kimura (1968) proposed that the variations found in organisms are formed from processes of mutation and genetic drift, not by natural selection, as was widespread. In genetic drift the mutations are random over time and lead to a more or less predictable result. That is, you know what will happen, but you do not know the exact trajectory of this event. From these ideas the neutral theory allowed hypotheses to be created for molecular substitutions. The null hypothesis will always be that the substitutions are neutral, that is, non-adaptive. The alternative hypothesis is that they are selective, that is, they have adaptive value. This last one generates some alteration that benefits the organism and this one is passed to the next generations. What is known today is that most mutations are deleterious, slightly deleterious, or neutral, mostly neutral. This means that: most mutations do not make a difference or generate some kind of change in the individual, let's say they are "silent".

- Kimura, M. 1968. Evolutionary Rate at the Molecular Level. Nature, 217:624.

Revisado por: Beatriz Gomes

O texto está muito bom, Rosana.
Frases na ordem direta, linguagem clara e concisa. A escrita em inglês está bem fluida, parabéns!


Ensaio 3 - 31/03/17

AUDIENCE: Graduate students

Effective population size deals with how many individuals are effectively contributing to the genetics of the next generations (Ballou & Foose, 1996). The measure of this parameter is made from the genetic diversity found in the alleles (Toro & Caballero, 2005). Within a population, the greater the number of heterozygotes, the more diverse it is (Ney, 1973). In a small population, heterozygosity is lost quickly, as genetic drift acts faster. In larger populations, the drift effect is more buffered and occurs more slowly. In these, genetic drift loses its "power" to fix new alleles. However, even in large populations, when there are individuals who interbreed, the tendency of this population is to become increasingly homozygous over time. Another important point to emphasize is that allele fixation is random in small populations. However, genetic analysis of subpopulations can "forge" a high heterozygosity that does not exist, which creates a bias in the interpretation of the data. Natural selection does not act on small populations. On the other hand, in large populations you can see that a small selective effect can cause significant changes in allele fixation.

- Ballou, J.D. & Foose, T.J. 1996. Demographic and geneticmanagement of captive populations. - In: Kleiman,D.G., Lumpkin, S., Allen, M., Harris, H. & Thompson,K. (Eds.); Wild mammals in captivity. Chicago, University of Chicago Press, USA, pp. 263-283.
- Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences USA, 70, 3321–3323.
- Toro, M. & Caballero, A. 2005. Characterization and conservation of genetic diversity in subdivided populations. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 360:1367–1378.

Revisado por: Giulia Ribeiro

The measure of this parameter is made from the genetic diversity found in the alleles (Toro & Caballero, 2005) - Voz passiva, ficou meio confuso. Eu talvez até repetiria o tamanho efetivo, para colocar a frase na ordem direta.
Within a population, the greater the number of heterozygotes, the more diverse it is (Ney, 1973) Aposto. Tambem ficaria melhor na ordem direta.
Eu me perdi um pouco em qual a mensagem central do seu texto. Talvez deixá-la clara logo no início.
Mas as ideias estão legais, acho que só seria uma questão de organizá-las melhor.


Ensaio 4 - 05/05/17

Historical reconstruction is considered a method/tool. From this method it is possible to understand the strengths and weaknesses of the hypothesis of work raised. There is a phenomenological structure that uses historical reconstruction in data analysis in order to generate a classification. Although reconstructions generate trees, this is not, a priori, the goal of the researcher. A phylogenetic tree can evidence several other observations and questions about its hypothesis and object of study, besides, only, to generate a classification of organisms/characters/biogeographic areas. Although most of the historical reconstructions refers to evolution, it is important to emphasize that the two processes are quite distinct and independent. Ohara (1993), brilliantly, compares the construction of a phylogenetic tree with the use of cartographic elements to draw a map. According to this author "since in the tree shows all the details of phylogeny, every tree is the selection from and the generalization of the totality of the events in the evolutionary past, just as every map is a generalization of the surface of the Earth."

- O'hara, R.J. 1993. Systematic generalization, historical fate and the species problem. Systematic Biology, 42:231-246.

Revisado por: Beatriz Gomes

Na minha opinião, seria interessante incluir um exemplo para a sentença "From this method it is possible to understand the strengths and weaknesses of the hypothesis of work raised.", algo como testar a monofilia de um gênero, daí com a reconstrução filogenética (ferramenta) se poderia refutar ou aceitar a hipótese de manter todos os terminais em um único gênero ou não, no caso, propor mudanças taxonômicas (objetivo do trabalho: classificação biológica).
Em síntese, o texto está bem escrito e objetivo.


Ensaio 5 - 12/05/17

The reconstruction of phylogenetic trees from an exhaustive search is usually computationally impractical, being most of them generated in a heuristic way. In the exhaustive search, the application builds all possible trees, makes all of them with relevant parameters and from there the program chooses the best one. However, this method is very limited in the number of terminals. If you use 20 letters (an analogy to nodes) you take about 10 years to analyze your data. However, in the heuristic search you can limit the parameters to be used in the analysis. In this type of search you work with a sample of the best possible trees and from this sample the program chooses the best one. In this type of search you give instructions for the algorithm to work. The molecular model, for example, presents 12 parameters (Kimura, 1980). The more parameters, the closer to reality your model is, however you assume more assumptions and the interpretation of your data becomes more complex.

- Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16:111-120.

Revisado por: Deyvid Amgarten

Boa sentença tópico Rosana, mostra logo de cara o tema do ensaio. O texto de maneira geral está bom, mas ao ler eu senti falta de uma concatenação dos pensamentos expressos nas frases. É aquilo de fluidez que o Daniel falou e que demora um pouco para pegar prática.
Fiz algumas observações pontuais que talvez ajudem:
- Na sentença tópico está faltando algo ligando as duas partes da sentença. Talvez "..is usually computationally impraticable, being most of them generated in a heuristic way".
- "…with relevant parameters and then the program chooses the best one".
- "The molecular model, for example, presents 12 parameters (Kimura, 1980)". Eu trocaria o "for example" pro final da frase.
- "…however you assume more assumptions…". Make more assumptions ficaria menos redundante.

Espero ter ajudado :)



Ensaio 6 - 19/05/17

Genomes are vulnerable to selfish genetic elements (SGEs). These elements increase their own transmission relative to the rest of the genome of an individual, but are neutral or detrimental to the individual as a whole (Werren, 2011). SGEs spread to populations distorting the transmission patterns proposed by Mendelian segregation (Hurst & Schilthuizen, 1998). Transposable elements are commonly considered "genomic parasites" and are one of the most well-known examples of SGEs. Their life cycle comprises dispersing into several species, increasing the number of copies, and perpetuating themselves in the host genome until they lose their replication capacity (Kajihara, 2010) .The selfish elements improve their own transmission in relation to other elements in a genome of individuals. This "genetic conflict" between selfish and other elements within the genome can be an engine for evolutionary change in organisms.

- Hurst, G. & Schilthuizen, M. 1998. Selfish genetic elements and speciation. Heredity, 80:2–8.
- Kajihara, D. 2010. Caracterização dos genes mustangem em gramíneas com ênfase no estudo funcional em cana-de-açúcar. Dissertação de mestrado, Instituto de Biociências, Universidade de São Paulo. 31p.
- Werren, J.H. 2011. Selfish genetic elements, genetic conflict, and evolutionary innovation. Proceedings of the National Academy of Sciences, 108:10863–10870.

Revisado por: Edgar Gamero

As sentencias são claras, estão escritas eloquentemente e por tanto dá entender o texto sem problema. Eu como leitor só fiquei com a dúvida de porque os transposable elements são mais conhecidos/estudados. Então, dependendo do público alvo você poderia ter escrito se é pela sua abundância, os efeitos que eles têm no hospedeiro, etc. Em geral, o texto está muito bom!


Ensaio 7 - 26/05/17

The difference between the models is the number of parameters that will be included in it. In the nucleotide model, for example, you have a maximum of 12 parameters for the base substitution rate. In the simple model (JC) you reduce the number of parameters, it will always be your null hypothesis. The complex model (GTR), on the other hand, will be your alternative hypothesis, with the various parameters that can be used. There are still other parameters that can be included in the model: base frequencies (F), invariant sites (I) and variation between sites (Gamma). Bear in mind that by adding gamma, you will add, at least, four more parameters to your model, making it more complex. Another important information is to know that using invariant sites parameter and gamma is redundant because in gamma you already have a zero-replacement rate. In a model you want to estimate the behavior of the parameters and how they vary. There is no right model, but a useful one for what you intend to develop (Box, 1976).

- Box, G.1976. Science and statistics. Journal of the American Statistical Association, 71:791–99.

Revisado por: Ana Laura

-No geral o texto apresenta frases curtas, como o recomendado. Isso é bom, lógico! No entanto, encontrei alguns problemas que listo abaixo:
-Não há Topic sentence, então o começo do texto é estranho, porque parece que falta algo antes daquilo.
-Você poderia ter adicionado um título ao seu ensaio também.
-Você deveria explicar o que significa o JC que você colocou entre parênteses, porque a ideia que se tem é que é a sigla para modelo simples. Você deveria também dizer que modelo simples é aquele modelo que estima apenas 1 parâmetro. A mesma ideia se tem quando você usa a sigla GTR. Você poderia dizer que o modelo mais complexo que estima 12 parâmetros é o denominado GTR, por exemplo. Assim eliminaria a ambiguidade.
-A redução de número de parâmetros é de quanto para quanto? Tem que tornar as informações mais explícitas, até porque você não disse qual é o público alvo do seu texto. Se for para um leigo, não entenderá praticamente nada. Se for para alguém que entende do assunto, terá que ficar supondo as coisas.
-Na frase “In a model you want to estimate the behavior of the parameters and how they vary” penso que estimar o comportamento dos parâmetros e o quanto eles variam seja uma redundância. No lugar de comportamento dos parâmetros, seria mais acertado dizer valores dos parâmetros, porque a variação em si já é o comportamento.


Ensaio 8 - 02/06/17

In phylogenetic reconstruction you use various search algorithms that help in building the best tree. In the hill-climbing the interactions seek to optimize the search criteria. On it, the program add one parameter at a time and then checks if the next one is better than the previous one, at the end the algorithm finds the best step. Before starting this process it is important to already have a tree built, as this will help start hill-climbing. Starting the analysis from a random place is very costly computationally. Most researchers build this tree before, using the Neighbor-Joing method. In some analyzes the algorithm can give you a wrong high point because it is greedy and can not pass the valley between the maximum point it encountered and the true maximum point. This is a problem with all search algorithms, they are all local, when they should be global, but only a quantum computer (which is being developed) can solve this question. We can, didactically, classify the search algorithms in two ways: explorers and refiners. Within the explorers we have the Quartet Puzzle that creates quartets and applies the Nearest Neighbor Interchange (NNI), in other words it always changes the neighbors. This is a fast algorithm that manages to explore a great spot of possibility but may not find the best tree. Many programs use it at the beginning of the process, but in the end they refine the analysis with other algorithms. Refiners are used to upset the algorithm and cause it to leave the site that it "thinks is the best" for the site that is actually the best one. They serve to explore more of the tree spaces because, as I said earlier, greed is constant in this group!

Revisado por: Giulia Ribeiro

Olá. Achei seu texto muito legal. Só talvez aí teriam informações para dois parágrafos. Isto porque você começa falando dos algoritmos de hill-climbing e depois você ainda fala dos algoritmos refinadores etc. É bastante informação.
Outra coisa, eu não sei o seu público alvo, mas o conceito de um espaço de árvores local e global não é tão óbvio de se entender. Então seria legal introduzir esse tema do espaço de árvores etc se for utilizar esses termos. Eu sabia, porque assisti a aula.
Algumas frases um pouco longas
Mas achei legal porque foi um bom resumo da aula


Ensaio 9 - 09/06/17

The theory of the red queen and the court jester do not explain, by themselves, all the events of speciation. The theory of the red queen is related to microevolution and to biotic events. It acts on smaller populations and on a smaller time scale. The good example of this theory is the "arms race" that occurs when phages parasite bacteria. Both will create invasion and defense structures that maintain the parasite-host relationship over time. The theory of the court jester, on the other hand, is tied to macroevolution and to abiotic events. It acts on a global scale over a longer period of time. It is related to climate, geographic and impact events on our planet. Ice ages and the meteorites that destroyed the dinosaurs are examples of this theory. However, despite this enormous adaptational appeal in most biological research, Venditti et al. (2010) argue that even speciation events can be neutral. The authors state that speciation is a result of stochastic changes in organisms and is little influenced by biotic and abiotic factors, as many argue. That is, the neutral theory also be behind these events and future works may reveal its importance to explain the emergence of new species in the nature.

- Venditti, C.; Meade, A. & Pagel, M. (2010) Phylogenies reveal new interpretation of speciation and the Red Queen. Nature, 463(7279): 349–352.


Ensaio 10 - 23/06/17

AVALIAÇÃO DA DISCIPLINA

Confesso que eu havia pensado que a disciplina teria um outro enfoque. Como eu pretendo fazer uma parte molecular no meu mestrado (se houver tempo!), eu pensei que a disciplina seria mais prática, que iria nos mostrar como usar ferramentas de análise de dados moleculares e a montar árvores filogenéticas baseadas nestes dados. Isto poderia me ajudar bastante em um dos objetivos da minha dissertação. As aulas acabaram sendo mais teóricas e confesso que fiquei perdida em vários pontos por nunca ter trabalhado com os programas abordados em sala de aula. Claro que as discussões me ajudaram muito e, hoje, já tenho uma bagagem de conhecimento sobre a temática muito maior e mais clara, mas esperava uma abordagem diferente. Não que as aulas foram ruins, ao contrário, foram muito enriquecedoras e me esclareceram muitas dúvidas, mas essa "má" interpretação da minha parte me fez pensar (querer!) que elas seriam desenvolvidas de uma forma mais prática do que teórica. Como eu falei anteriormente, mesmo lendo o material disponibilizado antes da aula, eu não conseguia entender alguns temas e ficava um pouco perdida nas discussões em sala de aula. Eu observava que alguns colegas, que já haviam trabalhado com as ferramentas/programas/modelos apresentados, conseguiam compreender facilmente o que o professor estava querendo abordar. Também me sentia um pouco insegura em tirar dúvidas, pois ficava parecendo que eu não tinha estudado e/ou prestado atenção na aula direito. Apesar de todas estas lamentações colocadas, eu gostei da disciplina neste formato também. Gostei da organização dos conteúdos, da dinâmica das aulas, do cronograma bem definido (adoro isso!), do modelo de postagem no blog e dos ensaios no final da aula. Praticar a escrita acadêmica me ajudou bastante e até mesmo corrigir meus colegas foi uma experiência muito produtiva pra mim. O que eu não gostei foi que o professor parou de trazer as criticas e sugestões dele ao longo do semestre, esses "insights" dos nossos textos sempre me ajudavam a melhorar meus parágrafos seguintes. O professor sempre foi muito solicito e aberto à novas discussões, nos estimulava a pensar e a debater nossos pontos de vista, mesmo que estes fossem "sem pé, nem cabeça". Eu me esforcei para acompanhar o nível da turma e fiquei muito feliz com minha evolução na disciplina, mas não acho que mereça 1 ponto na minha autoavaliação por conta dos meus atrasos constantes. Contudo, participei das discussões, fiz vários questionamentos, lia os artigos antes da aula e me dediquei 100% na primeira avaliação, então eu acho que mereço meus 0,9. Espero ter colaborado com meus apontamentos!

Grata.

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