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Poster project conclusion

Submitted by briangriffin on Thu, 12/07/2017 - 21:16

                This experiment did not result in a statistically significant difference in growth between the control group and the planaria living in the 31˚C water. The T-Test resulted in a P-Value of 0.999 meaning that it is highly likely that the variation observed in growth differences was due to chance. This result could be due to the time allotted for the experiment. With only 13 days, the planaria did not have a significant time to regenerate. This lead to observed growth of only about 0-0.1 cm, which was about 0.5 cm away from the planaria regenerating to their initial length. Also using a more accurate form of measuring could help the statistical analysis be more accurate we rounded to the nearest 100 mm. If we also had a larger sample size in each control it could lead to a stronger statistical analysis. Thus giving us a more accurate understanding of the effect of temperature on regeneration. 

Thesis intro P2 pp

Submitted by briangriffin on Thu, 12/07/2017 - 21:15

              In Europe, BWA does not have a negative effect on its hosts. However, North American firs did not co-evolve with BWA which causes a hypersensitive reaction to its feeding. This results in grouting and the formation of “redwood”. Grouting describes the swelling at the branch nodes and the stunting of terminal growth; it results in loss of branch growth and an overall decline in health. Redwood refers to the reddish-brown coloration of the wood underneath the bark due to mass infestation on the main stem. This results in the decrease of water flow through the stems. After about two to three years of mass infestation in the stem, the host tree typically dies 

Thesis Into microsatellites

Submitted by briangriffin on Wed, 12/06/2017 - 13:02

             Microsatellites have been used widely to study population genetics of invasive pests. Microsatellites are tandem repeats of 2-6 nucleotides found throughout the nuclear genome. There is a high mutation rate among these loci due to slippage and proofreading errors, which occur at an average rate of 5*10-4 nucleotides per generation. Microsatellites follow simple Mendelian inheritance and are selectively neutral. Together this means that these loci are mutating quickly and these accumulated mutations are passed on to the offspring without any preference. This allows researchers to create fine scale phylogenetic trees of different populations and test for population genetic processes such as the presence or absence of sexual reproduction. For statistical power, multiple loci are used for more reliable inferences. Potential loci must pass through a screening process to eliminate errors. This includes: conforming to Hardy-Weinberg Equilibrium, eliminating possible linkage among loci, detecting homoplasy, and confirming that the loci are selected neutrally.

Thesis methods P3

Submitted by briangriffin on Tue, 12/05/2017 - 15:59

                        DNA was extracted from individual BWA specimen with the Omega Mag-Bind Blood and Tissue DNA extract kit following the provided protocol. For each sample, 19 loci were amplified using the following protocol. A master mix was set up for each locus with the ratio of, 6.15 µL of water, 2.5 µL of GoTaq 5x Flexi Buffer, 1.25 µL of 10 µM New England Biolabs dNTPs, 1 µL of MgCl2, 0.25 µL of the forward primer, 0.25 µL of the reverse primer, and 0.1 µL of the GoTaq Flexi Taq polymerase. The master mix was added to the Bio Rad 96 well plate with the volume of 11.5 µL per well. 1 µL of purified DNA was added to each well.  The plate was then placed in the Bio Rad T100 thermal cycler with the following protocol, 2 minutes at 95˚C, 5 cycles of 45 seconds at 95˚C, 30 seconds starting at 61˚C and decreasing by 2˚C every cycle, and 45 seconds at 72˚C. Then 25 cycles of 45 seconds at 95˚C, 30 seconds at 51˚C, and 45 seconds at 72˚C. Lastly a final extension step of 2 minutes at 72˚C. To prepare the PCR products for fragment analysis, the samples were put into groups based on the tag on the forward primer. Primers 1-5 were placed into group 1, primers 6-9 were placed into group 2, primers 10-14 were placed into group 3 and primers 15-19 were placed into group 4. 1 µL of each PCR product was added to another 96 well plate into their respective groups. Highly deionized formamide was added into each well. Groups 1, 3, and 4 received 5 µL of formamide for each sample and group 2 received 6 µL of formamide for each sample. These products were sent to The Yale University DNA analysis facility for Fragment Analysis using the Liz500 size standard.

Multiple Alignment analysis pp

Submitted by briangriffin on Thu, 11/30/2017 - 17:29

               Sequences of the Foxp2 gene from diverse taxa were analyzed using multiple alignment. The multiple alignment tool allows for you to align multiple sequences at once, while 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. This conclusion was made possible by the convience of the multiple alignment tool.

 

Microsatellite and ecology

Submitted by briangriffin on Thu, 11/30/2017 - 17:16

               The use of microsatellites has been used widely in the field of ecology to study things such as population genetics. Microsatellites are tandem repeats of 2-6 nucleotides found throughout the nuclear genome. There is a high mutation rate among these loci due to slippage and proofreading errors. These mistakes in DNA replication at these repetitive sites occur at an average rate of 5*10-4. Microsatellites follow simple Mendelian inheritance and are neutrally selected. This means that these loci are mutating quickly and these accumulated mutations are passed on to the offspring without any preference. This allows researchers to create fine scale phylogenetic trees of different populations. These traits make microsatellites very helpful in the study of colonization of BWA. For statistical accuracy, multiple loci are used for more reliable data. The selected loci must pass through a screening process to eliminate errors. This includes conforming to Hardy-Weinberg Equilibrium, eliminating possible linkage of two loci, detecting homoplasy, and confirming that the loci are selected neutrally and follow Mendelian inheritance 

Thesis intro P2

Submitted by briangriffin on Thu, 11/30/2017 - 17:14

              In Europe, this species does not have such a damaging effect on its host. In North America the firs have a hypersensitive reaction to the feeding of this organism. The feeding on the host results in grouting and the formation of redwood. Grouting describes the swelling at the branch nodes and the stunting of terminal growth. This symptom results in loss of branch growth and an overall decline in health. Redwood refers to the reddish-brown coloration of the wood underneath the bark due to mass infestation on the main stem. This results in the decrease of water flow through the stems. After about two to three years of mass infestation in the stem, the host dies.

Thesis intro P1

Submitted by briangriffin on Tue, 11/28/2017 - 12:48

Adelges piceae, commonly known as balsam woolly adelgid (BWA), is an herbivorous invasive pest in North America. This species of aphid uses balsam firs as its host and leads to damage and death of the host plant. Balsam woolly adelgid is native to Europe, but since about 1900, this species has been creating problems in North America. The first time this species was noted in North America was in Maine in 1908. Later reports, placed this species across North America from California to Virginia. BWA is now found everywhere its host tree is found, excluding the Great Lakes area and central Canada.

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. 

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