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Submitted by jiadam on Wed, 05/03/2017 - 14:29

The Methods project was one of the first project we started on and I have to admit I was not entirely sure what to expect or what was expected of me. I’ve written methods sections before, but it was usually just the actual procedure in my own words. Writing methods for the moss project provided its challenges because I was not sure what the most important things to write about where and what details did I need to include.

I wrote about the research I did before actually going out to look for moss, but that was irrelevant and I failed to mention details about the orientation and scaling of the figures which proved to be critical in the differences between the original and replicated figure. When it came time to do the project and actually write the methods, I succeed in some aspect and did not succeed in others. While I believed I had a grasp understanding of the difference between inferences and differences, my writing showed the latter and my actual methods provided irrelevant detail. I did write a results section with a lot of differences and the organization was good, but the organization for the discussion section was not.

journal

Submitted by jiadam on Wed, 05/03/2017 - 10:49

312 was a class that I believed I learned a lot from and developed as writer because of this class. I think I also learned a lot about who I am as a learner and what type of learning style I prefer just due to the small enclosed space and nature of the class. With each project brought new challenges and I believe I rose to the occasion on each and everyone. Working solo on the methods project and in a group setting for both the proposal and the actual group project provided a stark dichotomy and really led to some introspection on different manners of writing and the level at which a biologist like myself would need to achieve at.

PP

Submitted by jiadam on Sun, 04/30/2017 - 21:43

Meselson-Stahl Experiment
This experiment utilized 2 different nitrogens isotopes because nitrogen is a huge component of nucleotides. They were 14N and 15N. 14N is the light nitrogen and is the most abundant on earth. This makes DNA less dense. 15N is the heavy nitrogen which is not as abundant and denser. They used two different nitrogens so that they can be separated by density where the lighter would rise to the top. 15N was placed in E.coli and E.coli replicated the DNA. Using density centrifugation, they were able to see the amount of each nitrogen and which nitrogen it was because of the differences in density. After the first round of replication, the DNA was in the middle of the test tube which can indicate semi-conservative or dispersive because each DNA molecule is half 14N and a half 15N. After the second round of replication, one set of daughter cells were intermediate (half 14N/15N) and the other was lighter which answer the question between semiconservative and dispersive. DNA is replicated semi-conservatively. After numerous rounds, the amount of 14N was significantly more than 15N.

journal

Submitted by jiadam on Sun, 04/30/2017 - 21:22

Nucleotide addition during DNA replication

It is known that DNA is always synthesized from 5’ to 3’ direction and not 3’ to 5’. The incoming nucleotides are added from the 3’ end of the nucleotide that was added previously. DNA polymerase is the actual enzyme that is used in replicating the DNA strand, but it needs a nucleotides already there that has a free 3’ hydroxyl group. Primase solves this problem because it can add an RNA primer without an existing 3’ OH group. The nucleotide that is being added is a deoxyribonucleoside triphosphate. The triphosphate gives the reaction energy to proceed. To make sure the nucleotides being added are the correct ones, there is complementary base pairing between the nucleotides. Cytosine and Guanine have three hydrogen bonds as opposed to two between thymine and adenine. When the deoxyribonucleoside triphosphate is brought in, a phosphate is let go and a hydrogen from the hydroxyl group on the 3’ end of the previous nucleotide is cleaved and a bond is formed. This interaction creates a phosphodiester bond.

journal

Submitted by jiadam on Thu, 04/27/2017 - 18:29

Methods:

The Morrill conservatory is the first location and the Durfee conservatory is the second to be observed indoors. Sylvan pond and Campus pond were observed outdoors. For each observation area, 2 sites of different measurements were examined. Humidity and temperature averages were gathered from online sources for the week. Moss with different physical features and morphology was observed for 15 minutes and pictures were taken of these. Inside, moss was found on the surface of the soil in plant pots and the plant stalks; whereas, moss outside was found among the outer edges of the water and at the bottoms of trees. The area in which the moss was found, the number of moss species found, the area (in meters), humidity averages, and temperature averages were all recorded in a data table.

journal

Submitted by jiadam on Thu, 04/27/2017 - 10:53

Introduction:

Bryophytes are a very diverse phylum containing approximately 12,000 different species. With such diversity comes a variety of ranges moss can live in (Lepp). These species participate in ecological interactions, such as mutualism, commensalism, or competition, with one another and with other plant and animal species, living in close proximity (Smith et al.). Moss species shape the environment they live in and, conversely, the environment shapes their growth and survival (Katschnig et al.). Thus, a critical point of study is how bryophyte diversity relates to the abiotic conditions of an environment (Isermann).

The project aims to explore the species diversity in bryophytes and identify how temperature and humidity affect the diversity present on the UMass Campus, a rural  setting. These factors were chosen because of the agricultural implications we can learn from studying the model organism like bryophytes. By looking at the differences in moss over a week span, it shows that the humidity and temperature inside and outside are truly important factors when it comes to diversity and abundance.

journal

Submitted by jiadam on Wed, 04/26/2017 - 15:52

Pre-rc

The pre-replication is a 6 subunit heterohexamer at the origin of replication which is the start point of replication. Because replication occurs bi-directionally, two replication fork go into separate directions to speed up the replication process. Budding yeast only have 16 chromosomes and around 300 origins. Humans have around 6 billion base pairs of DNA and need much more origins of replication to get replication done in a quick manner. As soon as the first origin of replication is fire, the cell is in S phase. Origins can fire at different times. Some fire early in S phase and others fire later towards the end of s phase. In each replication fork, each strand is a template for a newly synthesized strand and the polymerases that are replicating the DNA are physically connected.

 

journal

Submitted by jiadam on Tue, 04/25/2017 - 11:45

Meselson-Stahl Experiment

This experiment used 2 different nitrogens because nitrogen is a huge component of nucleotides, 14N and 15N. 14N is the light nitrogen and is the most abundant on earth. This  makes DNA less dense. 15N is the heavy nitrogen which is not as abundant and more dense. They used two different nitrogens so that they can be separated by density. 15N was placed in E.coli and E.coli replicated the DNA. Using density centrifugation, they were able to see the amount of nitrogen and which nitrogen it was because of the differences in density. After the first round of replication, the DNA was in the middle of the test tube which can indicate semi conservative or dispersive because each DNA molecule is half 14N and half 15N. After the second round of replication, one set of daughter cells were intermediate(half 14N/15N) and the other was lighter which answer the question between semiconservative and dispersive. DNA is replicated semiconservatively. After numerous rounds, the amount of 14N was significantly more than 15N.

journal

Submitted by jiadam on Tue, 04/25/2017 - 11:16

How is DNA replicated?

There were three postulates as to how DNA was replicated. The first was semi-conservatively where both strands of DNA are used as template to to 2 new replicated strands. In this methods, in each new helix, one would have the parent template strand and a newly synthesized daughter strands. The conservative postulate was that both strands were used as DNA templates and as soon as replication was completed, the template strands would return to each other and the newly synthesized strands would form a new helix that has no old DNA. The last postulate was dispersive, where DNA is split into different pieces due to unwinding a double helix would cause too much supercoiling and tension at the far end, The DNA would get replicated and put back together with a mixture of parental and daughter DNA interspersed with each other. It was proven that DNA was replicated semiconservatively by Meselson-Stahl.

pp

Submitted by jiadam on Sun, 04/23/2017 - 16:54

DNA structure

DNA is known to have a double helix structure, but it is not common knowledge that it normally has a right handed spiral and contains major and minor grooves. The major grooves for DNA are where the sequence-specific DNA binding proteins bind and have access to the nucleotides which for allows for post translational modifications. The minor groove is where non-specific DNA binding proteins have access to the DNA, but more specifically to the sugar-phosphate backbone. DNA is made up of nucleotides and each nucleotide has a phosphate group, a 5 carbon deoxyribose sugar and nitrogenous bases. Each strand of DNA is a polymer because it is a chain of nucleotide monomers. The strands run antiparallel and form hydrogen bonds between each other. CG has 3 hydrogen bonds whereas AT only has 2. If they ran parallel, the bases would not form hydrogen bonds. Chargaff’s rule states that adenine binds with thymine and cytosine binds with guanine.

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