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Table of Contents
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Ensaio Opcional - Aula 1 - 12 de Março de 2019
Transcription and translation mechanism in eucaryotic: what is the difference from the colinearity hypothesis?
Advances of molecular studies in the last decades demonstrate the simplicity and limits of the sequential hypothesis - also known as colinearity - postulated by Francis Crick in 1958. Crick's hypothesis suggests that linear nucleotide sequences always encode a single protein. However, experiments realized after 1970 showed that colinearity rarely occur in eukaryotic genomes. The eukaryotic organisms generally exhibit alternatives approachs as the: (i) existence of splicing, which is explained as the cut off of introns sequences among the transcriptions units; (ii) occurence of alternative splicing, which is defined as the harvest and maintenance of exons and introns, and are related to the acquisition of different mRNA molecules from an single transcription unit; and (iii) translation of the mRNA sequence in different RNA type - as snRNA - or structures with undiscovered functions. Thus, the initial quotation proposed by Crick could be readjusted and postulate that: linear nucleotide sequences could produce different types of RNA sequences, which can encode different proteins or another genetic structures.
Reference: Pray, L. (2008). What is a gene? Colinearity and transcription units. Nature Education, 1 (1): 97.
Ensaio 1 - Correção do Ensaio Opcional- Aula 2 - 19 de Março de 2019
Correção por Alvaro
Transcription and translation mechanism in eucaryotic: what is the difference from the colinearity hypothesis?
Advances of molecular studies in the last decades demonstrate the simplicity and limits of the colinearity hypothesis. This hypothesis suggests that linear nucleotide sequences always encode a single protein. However, colinearity rarely occur in eukaryotic genomes since those generally exhibit alternatives approaches as the: (i) existence of splicing, which is explained as the cut off of introns sequences among the transcriptions units; (ii) occurence of alternative splicing, which is defined as the harvest and maintenance of exons and introns, and are related to the acquisition of different mRNA molecules from a single transcription unit; and (iii) translation of the mRNA sequence in different RNA type (as snRNA) or structures with undiscovered functions. Therefore, linear nucleotide sequences can encode different proteins or another genetic structures.
Reference: Pray, L. (2008). What is a gene? Colinearity and transcription units. Nature Education, 1 (1): 97.
Ensaio 2 - Aula 3 - 26 de Março de 2019
Written by Igor Salles de Oliveira
Genetic drift and natural selection in molecular evolution
Rates of non-synonimous and synonimous substitutions help the understanding of sthocastics events. The ratio of non-synonimous (nd) by synonimous (ns) substitutions reveal genetic signals. The genetic signals are associated with events as genetic drift or natural selection. Neutrality implies an random distribution of nd and ns in the gene/genome. Genetic drift act to maintain the neutrality. However, an unequal distribution of nd or ns indicate the action of natural selection. Purifying selection led to high values of ns in relation to nd. Adaptative selection led to low values of ns in relation to nd.
OBS : I tried to: (i) expose the ideias in a concise manner; and (ii) reduce the lenght of phrases.
Comentários do Ensaio 2- Aula 4 - 02 de Abril de 2019
Correção por Daniel Castro Pereira
Pontos:
1. Ideias foram expostas de maneira concisa;
2. Frases estão curtas e fáceis de entender. Porém, algumas frases poderiam estar conectadas a outras, por meio de conjunções ou outros elementos de ligação;
3. Tomar cuidado com afirmações que determinam uma função a algo ("Genetic drift act to maintain the neutrality."). É mais adequado enxergar a neutralidade como consequência da deriva genética, e não como uma função da deriva. Uma sugestão de reformulação dessa frase seria: "Neutrality may be a consequence of genetic drift".
Ensaio 3 - Aula 06 - 30 de Abril de 2019
Historical reconstruction as an tool to understand evolutionary patterns
Historical reconstruction is a powerful tool to rebuild and sort evolutionary patterns. Historical reconstruction is a method which relies on obtaining, analyzing and sorting of the evolutionary patterns through the hypothetical common ancestor between the lineages. The realibility of the historical reconstruction is related, for example, to the number of markers used and unbiased sampling. A recent review among domestical dogs breeds describes how the relationship among recent lineages was elucidated on the basis of historical reconstructions using single nucleotides polymorphism[1]. In conclusion, despite the existence of limitations, historical reconstruction is the most robust method to infer evolutionary patterns among representatives.
Reference: Freedman, A. H.; Lohmueller, K. E.; Wayne, R. K. (2016). Evolutionary history, selective sweeps and deleterious variation in the dog. Annual Review of Ecology, Evolution, and Systematics, 47: 73 - 96.
Correção realizada por Manuel em 07/05/2019
- O texto está muito bem escrito, explicativo e com exemplo de uso do tópico abordado.
- Possui mínimos errinhos bobos de inglês.
- Segue um texto com a inversão da conclusão com a sentença tópico. É uma ideia a qual achei que funciona um pouquinho melhor em um texto já bem escrito.
Historical reconstruction is the most robust method to infer evolutionary patterns among representatives. It is a method which relies on obtaining, analyzing and sorting evolutionary patterns among lineages through a hypothetical common ancestor. The reliability of the historical reconstruction depends on the number of markers used and unbiased sampling. A recent review studying domestical dogs breeds describes how the relationship among recent lineages was elucidated on the basis of historical reconstructions using single nucleotides polymorphism[1]. In conclusion, despite the existence of limitations, historical reconstruction is a powerful tool to rebuild and sort evolutionary patterns.
Considerações e autoavaliação dos ensaios apresentados até o presente momento - dia 14 de Abril de 2019
Qual a minha dificuldade ao escrever os ensaios:
Percebi que ao longo dos ensaios há uma tendência em manter frases longas, com dificuldade em organizar as ideias em frases curtas e utilizando conectivos.
Qual a dificuldade dos colegas de turma ao escrever os ensaios:
Percebi que em quase todos os ensaios há uma dificuldade em se manter o direcionamento do texto, faltando exemplificações. Adicionalmente, existe uma dificuldade, tal como a minha, em escrever frases curtas e manter clara as ideias desejadas.
Ensaio 04 - Aula do dia 21 de Maio de 2019
Models of nucleotide rates substitutions in historical reconstructions
The phylogenetics approachs use explicity or implicit an evolutionary model which improve the accuracy of historical reconstruction. Four molecular methods are used to infer historical reconstructions : (i) the UPMGA; (ii) the Neighbor Joining; (iii) the Maximum Likehood; and (iv) the Bayesian. The UPMGA takes on implicitly the existence of a model with identical rates of nucleotide substitutions. In the other hands, the others three methods apply algorithms to identify the better model which explain the data. Therefore, explaining the model used on the historical reconstruction. A review of molecular models of nucleotide rates substitutions stands out the existence of 24 kinds of molecular models ¹. Thereafter, the accuracy of the results relies on the complexity of each models ¹. In conclusion, all the molecular historical reconstruction approaches are done in the basis of molecular models of nucleotide rates substitutions.
Reference:
¹ Pomada, David. (2009). Selecting models of evolution. 345 - 361p. In: Lemey, P.; Salemi, M.; Vandamme, Anne-Mieke. (2009). The Phylogenetic Handbook: A pratical approach to phylogenetic analysis and hypothesis testing. 2ed. Cambridge Univeristy press. 723p.
Ensaio 05 - Aula do dia 28 de Maio de 2019
Pre-writting of the final essay: Outline.
[[==]]
Possible Questions:
1) Porquê fazemos reconstruções históricas?
2) Utilização de modelos em ciência com enfoque na reconstrução histórica.
3) O papel da reconstrução histórica na era do "Big Data".
4) O relógio molecular: teoria e prática.
5) Ainda existe espaço para os métodos fenéticos na biologia moderna?
[[/==]]
Chosen theme:
1) Porquê fazemos reconstruções históricas?
Outline:
Title: The use of historical reconstruction to determined hybrids zones and new species in Bothrops neuwiedi complex.
1 - Introduce the importance of the historical reconstruction. Trying to exposed the main objective of these analysis and to introduce the method.
2 - Introduce the complexity of the the Bothrops neuwiedi complex.
3 - Described the used to delimited possible hibridization zones. And how Carrasco resolve it.
4 - Implications of these delimitations.
Ensaio 06 - Aula do dia 02 de Junho de 2019.
Pre-writting of the final essay: Topic sentences.
Chosen theme:
1) Porquê fazemos reconstruções históricas?
Title: The use of historical reconstruction to determined hybrids zones and new species in Bothrops neuwiedi complex.
1 - Topic sentence: Historical reconstruction were used to infer evolutionary patterns and process.
Description: Herein I would like to introduce the concept of historical reconstruction. Followed by sentences which elucitade the
2 - Hybridization is a common event shaping snakes evolution.
Description: Herein I would like to introduce the problem of hybritization describing how to it is
3 - Historical reconstructions allow the delimitation of hybrid zones. Introduce the complexity of the the Bothrops neuwiedi complex.
Description: Introduce the complexity of the the Bothrops neuwiedi complex + Machado et al 2014.
4 - Described the used to delimited possible hibridization zones. And how Carrasco resolve it.
Description:
5 - Implications of these delimitations.
Description:
Peer review suggestion: Although hybrid zones interferred in the evolutionary patterns in snakes, the application of historical reconstruction don't delimit the hybrid zone. Therefore, I suggest the theme shift to: Species delimitation in Bothrops neuwiedi complex based on historical reconstructions.
1 - Description: Historical reconstruction were used to infer evolutionary patterns and process.
2 - Description: Use of taxony versus phylogenetics to resolve snakes evolution.
3 - Description: The problems of Bothrops neuwiedi complex groups.
4 - Description: O uso da filogenia no complexo Bothrops neuwiedi.
5 - Description: Conclusion to highlighted the use of historical reconstruction to species delimitation.
Auto avaliação e avaliação da disciplina
Autoavaliação
A nota reflete minha autoavaliação é 0.7. Ao me escrever na disciplina, eu esperava desenvolver habilidades, competências e conhecimentos que se relacionassem à reconstrução filogenética. Ao longo da disciplina consegui reorganizar e reforçar temas básicos, linkando esses temas com as práticas a serem desenvolvidas no meu projeto. Pude ampliar minhas técnicas de escrita científica, identificando minhas dificuldade e facilidades na escrita científica e na escrita da lingua inglesa. Porém, percebo que deixei de me esforçar tanto ao longo das disciplinas quando vi que havia uma falta de discussão acerca dos artigos propostos. Além disso, acredito que participei pouco da disciplina, devido a uma dificuldade maior saber expor minhas ideias e colocações em palavras. Por isso, acredito que uma autoavaliação de nota 0.7 é condizente com os pontos positivos e negativos que desenvolvi ao longo do semestre.
Avaliação
A minha avaliação da disciplina é boa. A disciplinas oferece pontos positivos e negativos. O fato de ter dito pouco contado com a temática de reconstrução filogenética me fez classificar a disciplina como mediana, com conceitos básicos e avançados. A oportunidade se treinar a escrita e desenvolver a mesma em outro idioma foi importante para a imersão no ambiente de escrita acadêmica. Porém, apesar dos pontos positivos senti falta de uma discussão guiada dos artigos que eram sugeridos. Pois, a discussão pode auxiliar a sedimentação e compreensão das próprias dúvidas acerca do assunto. Minha sugestão seria fazer com que os alunos conduzam a discussão de cada temática, pois a discussão pode explorar pontos não explorados pela visão canônica. Desse modo, acredito que a disciplina esteja em um bom formado e que haveria um melhor desenvolvimento se explore mais a discussão dos artigos.