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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.

journal

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

Gliding assay

Gliding assay are used sometimes an in vitro method to study motor function on microtubules. To make one, you need a cover slip and purified kinesin motors are placed on the bottom of the over slip. Microtubules and kinesins are placed on assay and they essentially glide. For this to be effective, you need fluorescence microscope, fluorescently labeled microtubules,and purified kinesin motor. The microtubules will move and with fluorescence, you can observe the directionality of the microtubules, the rate of movement of the kinesin, and what’s needed for kinesin function. Scientist used this in an experiment with eg5 a kinesin motor and a protein TPX2.

journal

Submitted by jiadam on Fri, 04/21/2017 - 00:42

Differences between DNA and RNA

The sugar for DNA and RNA are different. In DNA on the 2’ carbon, there is a hydrogen as oppose to the RNA which contains an additional hydroxyl group. Therefore in RNA, the sugar is called a ribose sugar and in DNA is a deoxyribose sugar. RNA is also less stable which is useful when it performs functions that need to be cleaved off after completed such as RNA primers, It is also known that while DNA is normal double stranded and RNA is single stranded, there are single stranded DNA and double stranded RNAs. Because of the extra hydrogen in the RNA sugar, it can be used as a catalyst because oxygen is used in various. They are called ribozymes, RNA differs from DNA because it replaces thymine for uracil as a nucleotide.

journal

Submitted by jiadam on Thu, 04/20/2017 - 21:31

DNA structure

DNA is known to have a double helix structure, but not many people know it is 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. 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. 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.

journal

Submitted by jiadam on Thu, 04/20/2017 - 11:31

Colchicine

When applied, the drug binds subunits and prevents polymerization. It is most useful at the beginning of mitosis because the microtubules that begin to grow will stop growing,depolymerize and fall apart. This mechanism is due to colchicine hydrolyzing all the GTP. Without free GTP, there is no free tubulin that can bind and continue polymerization. Colchicine is mostly used as a treatment for gout because it is able to stop neutrophils which are a type of white blood cell. Neutrophil are useful in inflammatory response so using colchicine is effective in providing an anti-inflammatory result. Vinblastine is similar in that it binds subunits and prevents polymerization as well which makes it a very useful drug in chemotherapy.

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