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Lab 1 Discussion Perfect paragraph

Submitted by briangriffin on Thu, 11/16/2017 - 20:57

            In this lab we extracted and purified DNA using the methods explained earlier. The extractions were successful in that the DNA was removed from the tissue and cells of Arabidopsis and isolated from the other macromolecules in the leaves. This was evident by the pellet at the bottom of our centrifuge tube. This pellet then dissolved in T10E1  which means that the pellet was in fact made of nucleic acids. My pellet did not fully dissolve in the T10E1 with the specified amount, I added extra T10E1 to finish dissolving the pellet. The pellet not fully dissolving could have been due to the fact that I had too high of a concentration of nucleic acids for the original 50 µL of T10E1 to dissolve, so with a better ratio of T10E1 to nucleic acids, the pellet was able to dissolve fully. 

Multiple Alignment analysis

Submitted by briangriffin on Thu, 11/16/2017 - 20:50
The multiple alignment allows for you to align multiple sequences at once, while the pairwise align only can align two sequences at one time.The sequence "DFLDSGLENFRAALEKN" that is unique to humans is probably an insertion in the homo sapien lineage after the divergence from chimps. This is probable because everything from fish to chimps do not contain this fragment in the foxp2 gene so its likely that this one lineage has an insertion rather than all the other lineages having a deletion. Also I know that foxp2 is believed to be involved with the evolution of language in humans so it makes more for this unique fragment to be unique in humans. 

BLAST analysis

Submitted by briangriffin on Mon, 11/13/2017 - 14:43
                There are 2 amino acid differences between Homo sapiens and Pan troglodytes, not including the gaps. There are 8 nucleotides different between the orthologs when not counting the gaps. There are more differences in the nucleotide alignment because a change in the nucleotide sequence does not necesssarily lead to a change in amino acid sequence. But when there is a change in amino acid sequence there is a change in structure and function of that gene, therefore conservation of the amino acid sequence is important. The gaps are in multiples of three and this is because these gaps are deletions or insertions of amino acids which are coded for by a string of three nucleotides. 

Persuasive statement Perfect paragraph

Submitted by briangriffin on Thu, 11/09/2017 - 18:45

              The breed of dog that should be given the vaccine is a husky. This type of dog should be saved because it is a relatively healthy. Many breeds of dogs have gone through tight bottlenecks over the past hundred years, which has led to many shared recessive diseases and phenotypic mutations. Huskies do not possess many of these phenotypic mutations such as stunted growth and a compressed face. Huskies are most phenotypically similar to the ancestors of all dogs. This provides us evidence that huskies contains a healthier genome than any other breed of dog. And with this healthier genome a bottleneck of one dog will lead to a better future population of dogs than any other breed.

proposal introduction

Submitted by briangriffin on Wed, 11/08/2017 - 19:07

Planaria are the model organism we plan to use in this experiment. This clade of animals has a behavioral response to light. This response is what we plan to study when we begin our research. We know that planarians avoid light and swim to darker areas of the water they are in. This could mean in the wild hiding under leaves and rocks, and also being more active at night. But what we plan to study is the effect of different wavelengths of visible light on the planarians. We want to know which wavelengths in the visible light spectrum cause greater photophobicity. We hypothesize that the organism will deviate less from the light stimulus when exposed to longer wavelengths, such as red, than when exposed to shorter wavelengths, such as purple. This hypothesis is based on the experiment in  “Planarian shows decision-making behavior in response to multiple stimuli by integrative brain function” carried out by Paskin et al.

Assignment 4 Perfect Paragraph

Submitted by briangriffin on Thu, 11/02/2017 - 16:19

                          The final outcome of this competitive interaction is that species 2 will out compete species 1. If the data point fell above the species 2 zero growth line then both population sizes would decrease but species 2 will stop decreasing in population size when it hits the zero growth isoclines for species 2 and the population size of species 1 will continue to decrease until it reaches its own zero growth isocline. If the data point falls in between the two isoclines then the population of species two will increase to the isocline and species 1 will decrease to the isocline. And lastly if the data point fell below both isoclines then both populations would increase in size until they both reach their respective isoclines. In all three scenarios, once the populations reach the zero growth isoclines, species 2's population will increase and species 1 will decrease until both reach the k2 anchor. This anchor is the carrying capacity for species 2 and is along the y axis meaning that species 1 has a population size of zero and the population size of species is the highest that it can reach in this environment.

Persuasive statement

Submitted by briangriffin on Tue, 10/31/2017 - 20:05

              The breed of dog that should be given the vaccine is a husky. This type of dog should be saved because it is a relatively healthy breed. Many breeds of dogs have gone through tight bottlenecks which has led to many shared recessive diseases and phenotypic mutations. Huskies do not possess many of these phenotypic mutations such as stunted growth and a compressed face. Huskies are more phenotypically similar to their wolf ancestors meaning that this breed contains a healthier genome. And with this healthier genome a bottleneck of one dog will lead to a better future population of dogs than any other breed.

287 Assignment 4

Submitted by briangriffin on Mon, 10/30/2017 - 16:23

                The final outcome of this competitive interaction is that species 2 will beat out species 1. If the data point fell above the species 2 line then both population sizes would decrease but species 2 will stop decreasing in population size when it hits the zero growth isoclines for species 2 and species 1 will continue to decrease population size until it reaches its own zero growth isocline. If the data point falls in between the two isoclines then the population of species two will increase to the isocline and species 1 will decrease to the isocline. And lastly if the data point fell below both isoclines then both population would increase in size until they both reach their respective isoclines. In all three scenarios, once the populations reach the zero growth isoclines, species 2 population will continue to increase and species 1 will decrease until both reach the k2 anchor. This anchor is the carrying capacity for species 2 and is along the y axis meaning that species 1 has a population size of zero.

Lab 1 Discusion

Submitted by briangriffin on Thu, 10/26/2017 - 17:06

                In this lab we extracted and purified data using the methods explained earlier. The extractions were successful in that the DNA was removed from the tissue and cells of Arabidopsis and isolated from the other macromolecules in the leaves. We could see this with a white pellet at the bottom of our tube. This pellet then dissolved in T10E1 which means that the pellet was in fact made of nucleic acids. My pellet did not fully dissolve in the T10E1 so I had to add extra which did dissolve the pellet. This might be because I had too high of a concentration of nucleic acids for the original 50 µL of T10E1 to dissolve so with a better ratio the pellet was able to dissolve fully. 

Planarian perfect paragraph

Submitted by briangriffin on Thu, 10/26/2017 - 16:53

                        Planarians are often found under rocks in freshwater. This behavior is possibly due to the Planarians escaping excessive light. This can explain the behavior of wall preference in Planarians. The wall preference of the planarians was tested in “Spontaneous Behaviors and Wall-Curvature Lead to Apparent Wall Preference in Planarian”. The experiment was done in a dark room with only red light, the planarians were placed in dishes for 600 seconds and allowed to move around freely within the dish. During this time period the dish was monitored with a camera. Then the footage was analyzed to find the wall and the center preference. These preferences being equal to the Time in each location divided by the total time of being in the dish. (Akiyama et al. 2015)

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