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Submitted by akoundinya on Sun, 11/26/2017 - 15:12

Telomeres are non-coding regions at the end of the DNA sequence. Because some end segments are lost in DNA replication, the telomere allows necessary sections of protein coding DNA to remain unharmed during multiple cell division cycles.

At the end of the chromosome, there is a section of DNA that does not get covered by an Okazaki fragment because the primer would fall beyond the chromosome's end. As a result, the ending sequences cannot be covered by an Okazaki fragment and does not get replaced by DNA (gets cut off).

Telomeres are single stranded overhangs at the end of the DNA sequence. However, a complementary strand is formed in DNA, creating a protective loop that protects telomeres from the DNA repair system.

Telomerase is a specialized DNA polymerase that uses an RNA template for DNA creation. First, telomerase binds to the RNA molecule that contains the sequence for the telomere (TTAGGG). Then it adds nucleotides to the overhanging strand, lengthening the telomere. After the strand is long enough, an RNA primer and DNA polymerase will create the other strand to produce double stranded DNA.

Germ cells need to provide all the necessary protein coding DNA as well as enough telomere to give rise to an offspring with a normal lifespan. If telomerase was not active in germ cells, then each generation would have a shorter lifespan than the previous.

Microtubules, Cohesion, and Codensins

Submitted by akoundinya on Sun, 10/29/2017 - 16:19

Microtubules maintain cell shape, help in cell division, as well as aid in vesicle transport throughout the cell. They provide the cell with a structure, so that the cells do not collapse.

Microtubule structures form many different complicated structures in cells. A single microtubule is a polymer that can bind to others to form spindle fibers. Microtubule doublets form the cilia in specific cell types. Microtubule triplets form the structures of centromeres as well as basal bodies. 

Polymerization and depolymerization is driven by GTP binding and hydrolysis on the beta-tubulin monomer. The polymerization and depolymerization events give microtubules a dynamic instability which allows them to find and bind to kinetochores, spindle poles, etc. as well as remain free for subunit exchange.

Microtubules have dynamic instability due to polymerization events as well as a large number of binding sites. This allows microtubules to grow and shrink as well as bind vesicles for transport. 

Cohesion is a sticky protein that holds the sister chromatids together in S phase when the chromosomes are duplicated. At the beginning of anaphase, the cohesion is broken down in order for the sister chromatids to be pulled apart.

Condensins help condense the DNA in the chromosomes. They exist in the center of sister chromatids, holding the DNA in a coiled, condensed state. Using ATP hydrolysis, Condensin coils DNA in a test tube.

Cytokinesis (cytoplasmic division) needs to happen after all chromosomes have been properly segregated. If this does not happen, extra chromosomes or missing chromosomes would exist in the daughter cells. This can lead to cell death or disease.

Centrosome duplication occurs in interphase, when the centrioles and other components are duplicated in anticipation for DNA replication. When mitosis starts, the centrosome complex is split in two and each centriole pair becomes part of seperate microtubule organizing centers which nucleates the microtubule structure called an aster. There are two asters that move to opposite sides of the cell and eventually form the two poles of the mitotic spindle that will seperate the sister chromatids.

In Class Assignment: Legend

Submitted by akoundinya on Fri, 10/20/2017 - 15:20


Figure 1-3. GPA vs. Gender- Based on the trends in the graphs, it is apparent that the majority of females have higher GPAs than males with a few exceptions. 

Figure 4-6. Gender vs. Hours Slept per Week- This chart shows that the female population slept a greater number of hours than the males on average. This is apparent from the female curve being shifted to the right of the male curve. This indicates that the max number of hours slept by both genders is similar, but more females on average slept more hours. 

Figure 7-9. Gender vs. Hours Studied per Week- This chart shows that the trend for amount of hours studied is quite similar in males and females. However, notice that the female curve is shifted over to the right of the male curve. This indicates that while the max number of hours studied by both genders was similar, on average, the female population had more members that studied a higher number of hours. Based on the rightward shifts of the female Sleep and Studying charts and the general trend of Females having higher GPAs, it is apparent that there is a correlation between the number of hours studied and slept and GPA. 


Submitted by akoundinya on Thu, 10/19/2017 - 02:32


The human body has limited regenerative abilities. However, other vertebrates such as salamanders have the ability to regenerate body parts such as their legs and tail. However, this ability still pales in comparison to the regenerative ability of Planaria. Planaria have the ability to regenerate their entire body structure including their Central Nervous System from a 1/279 slice of their original body. Their regenerative ability has been studied extensively for the past 200 years. However, with the creation of next generation sequencing and our new knowledge of RNAi activity, Planaria regeneration can now be studied on a molecular level. Because Planaria have a small body size and has 4 diploid chromosomes, they can be easily studied in large populations at a relatively low cost. They also share similar functional proteins with humans and can be easily studied in vivo using RNA interference administered through injection or introducing RNA double strands to the media. This allows us to place chemical markers on the proteins necessary for the regeneration of specific Planaria body structures. Planaria serve as a model organism that contains a large amount of adult pluripotent stem cells. In terms of the next generation of medicine, studying the chemical and biological basis for Planaria regeneration can enable us to discover potential pathways for human cell regeneration.

This research article was very interesting because it specifically names several proteins in the Wnt/β-catenin pathway that can be altered using RNA interference to cause different effects in the regeneration of Planaria. Given the improvements in sequencing technology and RNAi experimentation, we can now identify specific proteins and pathways that cause the regeneration of specific body structures. Needless to say, this is extremely important in the study of cell regeneration as well as the future of human medicine.       



Research Article

Gentile, Luca, Francesc Cebrià, and Kerstin Bartscherer. “The Planarian Flatworm: An in Vivo Model for Stem Cell Biology and Nervous System Regeneration.” Disease Models & Mechanisms 4.1 (2011): 12–19. PMC. Web. 19 Oct. 2017.


Summary Article

The Editors of Encyclopædia Britannica. “Planarian.” Encyclopædia Britannica, Encyclopædia Britannica, inc., 25 Apr. 2016,

Abstract Draft

Submitted by akoundinya on Sun, 10/15/2017 - 19:36

The Harmonia Axyridis is the most commonly recognizable species of Ladybug in Massachusetts. It thrives in the autumn forests of Western Mass, before traveling indoors for the winter. As a result, these beautiful red and black spotted beetles can be found inside Umass dorms as well as outside in Nature. The point of this manuscript is to demonstrate the necessity of being able to write an accurate and concise Methods section that will allow other scientists to successfully complete the same experiment or gather the same experimental figures as I have. By choosing a commonly identifiable bug species native to this area, it should not be too difficult for a student to acquire pictures of it from simply walking around campus or the dorms. By following my own methods, I will create a Figure that details the anatomical structures of the beetle. Then, another student will follow my methods, create a Figure, and I shall compare their replicate figure to my original. The differences will be noted and the reasoning behind the differences will be analyzed.    


Perfect Para: Cell Biology Notes

Submitted by akoundinya on Sun, 10/15/2017 - 19:13

Checkpoints work as breaks in the cell cycle, allowing for a multi-step control of the cycle's stages. Mutations in the breaks allows for cell pathways to activate without signals, like a car accelerating without breaks.

In order for the cell replication process to be successful, the DNA code must be uncompromised and DNA checks must occur. DNA must be stable, functional, and must be able to be replicated for the cell cycle to progress.

In S phase, DNA is replicated and histone proteins are created (to wrap DNA around). In G2 phase, the cell starts to split and DNA segregates. 

Cells that are specially differentiated stay in the G0 or quiescence-phase. Here, cells like neurons and red blood cells serve specific tasks and do not need to replicate. However, they can be reverted back to a normal G1 stage when given proper signaling. If damaged, they simply enter apoptosis from G0. 

CDKs or Cycline dependent kinases are essential in cell cycle control. Kinases transfer phosphate groups from ATP to proteins in a pathway in order to cause an activating change in conformation. Kinases activate proteins, by phosphorylating them.  

Post-translational modifications are changes made to a protein's structure after it was originally created by ribosomes in the ER. These changes can involve Phosphorylation or dephosphorylation, ubiquitination, methylation, or the addition of functional groups or structural changes made that alter the protein's structure/function.

3 classes of CDKS: 1) G1/S CDKs bind and cause DNA replication 2) S phase CDKs are essential in regulating DNA replication 3) Mitose-cyclins promote and drive mitosis.

Rb is a protein that when mutated, causes tumor formation in the eye (retinoblastoma). Rb is an inhibitor of the cell cycle progression. Without a functional Rb, the cell will not be able stop itself from replicating.

p53 is a cell cycle checkpoint. They halt the cell cycle if they detect DNA damage. External factors such as UV rays can cause DNA mutations, but also mistakes in replication or segregation can also cause DNA damage. Damage can be fixed using specific proteins but p53 stops the cell cycle and allows for DNA damage control. 

Mutations in p53 can allow a cell with DNA damage to successfully replicate. This can result in cells that are missing DNA segments or are damaged in some way. In many cases, this can lead to cells that are cancerous in nature because they can replicate continuously despite having DNA damage.

Perfect Para: Comic Lit Paper

Submitted by akoundinya on Sun, 10/15/2017 - 19:05

Pre-Depression era American had a stronger connection to the notion of free enterprise, hard work, and individualist success. However, the years of the Great Depression spread fear and disillusionment in American society; as society questioned the flawed institutions that saw millions starving on the street. Outlaw and gangster films started to become significantly more popular because the masses still admired the individual spirit and the motivation to succeed where normal economic institutions have failed. During this time of strife, the American people strongly identified with anti-heroes that defied a broken system and profited, despite the odds. At this time of economic chaos, the desire to gain power and upward mobility was stronger than ever. And the American public liked the idea of superhuman powers that could make the pursuit of money and fame easier. Soon, all sorts of mental and physical supermen started appearing in newspaper comics and sci-fi pulp magazines. In fact, Andrae argues that the populace liked super heroes that had so much power and wealth that they physically posed a threat to society; a feeling that stemmed from a distrust socio-economic system of the day. With the depression came a new view on the financial situation of the country. While power and wealth was attractive to the masses, invariably, a superman who has both would be hated and blamed for taking advantage of the institutions and being a factor in the collapse of the economic system in the first place. Businessmen who existed in positions of society with power were the ones whose irresponsible actions led to the crash of the market and the Depression in the first place. However, during this time, Americans still had a strong sense of individuality and the American dream was to become successful with your own two hands. Thus, Superheroes in literature were generally defined as strong warriors for social justice that at many times, were at odds with the law. Siegel’s and Shuster’s original Depression era Superman was lawless, powerful, and wanted by police. And while he kills if necessary, Superman had a strong moral code to not use his powers for money or evil. This strong moral code resonated with public’s need for impartial justice in a system with corruption in unions, political parties, and government officials. 

Methods: Ladybug

Submitted by akoundinya on Sun, 10/15/2017 - 18:05

Coccinellidae is the name of a family of beetles that contains over 6,000 species found worldwide. And while Coccinellidae beetles are known by many different names, the red and black spotted Ladybugs are the most famous Coccinellidae species in North America. In Massachusetts, there are 3 different Ladybug species. The first is called the convergent ladybug (Hippodamia convergen) which sports a long body length and between 8 and 12 spots. Another, technically non-native species, is the seven-spotted ladybug (Coccinella septempunctata). However, neither of these two ladybug species are as common or as recognizable as the Harmonia axyridis, which was introduced from Asia. The Harmonia axyridis has an almost perfectly hemispherical body shape, has a bright red shell (Elytra) and as many as 19 black spots. The Ladybugs that I found around my dorm in Sylvan Residential Area at Umass and on plants outside of the buildings were undeniably Harmonia axyridis, considering the hemispherical body shape and the number of spots on the shell. Harmonia axyridis adults have an average lifespan of 1 month and are considered to be omnivores that feed on aphids and mites as well as flower nectar, tree sap, and a variety of different fungi. They appear in their adult form in the autumn when evening temperatures are in the 60 degree Fahrenheit range, and night temperatures drop to 40s and 50s. At this time, the Ladybugs search for warm indoor locations to survive the cold night temperatures and the incoming winter. In September and October, the Harmonia axyridis thrive in the densely wooded environment of Western Massachusetts. As such, they can be readily found in Umass dorm buildings as well as outside in nature. In Figure A, we have the top down view of a Harmonia axyridis that I found in my room. It’s distinguishing features of a circular shaped body and 18 spots are clear indicators of its species and differentiate this ladybug from its cousin species. Figure B is also a top down view of a Harmonia axyridis that is attached to the ceiling of my room. Ladybugs have wings that allow them to fly to great heights and they also have legs that have tiny hairs on them that allow the bugs to adhere to ceilings and walls. Figure B also shows a small amount of fecal matter behind the posterior end of the Ladybug. Figure C1 shows a ladybug that I found crawling on my desk. The picture was taken in front of the ladybug, looking down at it. Figure C2 is a larger version of C1, but with the anatomy of the ladybug labeled including the pronotum, antennae, legs, head, elytra, wings, and eyes.



Perfect Para: Cell signal notes

Submitted by akoundinya on Thu, 09/21/2017 - 19:15

Extracellular signaling is essential to the function of cells in the human body. While transcription of DNA in the nucleus and translation into proteins in the ribosomes are essential drivers of cellular function, signals outside the cell have a major impact on cell signaling. While stimuli such as light, odors, tastes, and mechanical stress all influence cell signaling, specific proteins called Hormones are substances produced within specific cells to regulate the function of other cells in different areas of the body. Extracellular signaling usually starts by a ligand binding to a receptor on the cell membrane of a cell. When a ligand binds to a receptor and causes a biological reaction in the cell, this ligand is known as an agonist. When a ligand binds to a receptor and causes no reaction other than the binding of the receptor, it is called an antagonist. After a ligand binds to the receptor and is absorbed into the cytoplasm, the ligand receptor can now interact with the G Protein. The name G protein came from its ability to bind to guanine nucleotides. After the ligand/receptor interact with the G protein, the G protein becomes activated and starts to activate other intermediate proteins called Secondary Messengers. These secondary messengers perform a variety of functions from aiding with the transcription of certain genes to the translation of specific proteins. Secondary messengers represent the intracellular reaction to the extracellular signal.

The Caterpillar in the Cup

Submitted by akoundinya on Fri, 09/08/2017 - 15:33

The organism appears to be a worm of a white-tan color with a segmented body. It has a brown head and a curled tail. It also appears to be the larval state of some sort of flying insect such as a moth or butterfly. For movement, the worm has 3 pairs of legs under the upper torso area right below its head. These 6 legs move constantly and allow the worm's upper body segments to move around. In the middle to lower torso, the worm has 4 pairs of legs that don't move as constantly. When the worm climbed on the ruler, it became apparent that the the middle 4 pairs of legs provide a type of suctioning support that allows the worm to stick to the surface of a leaf despite gravity. The worm usually stays in a somewhat curled state, most likely as a strategy to become less visible to potential predators. However, it its fully extended state, the worm was approximately 2 cm in length. The worm has tiny hairs all along the length of its body. These hairs allow for sensory detection of the environment and allows the worm to react to stimuli that it cannot see. The worm reacts quickly to touch and becomes visibly agitated and moves away from stimuli. The worm does not have any features that look like eyes but I assume that even if it has eyes on the front of its head, the worm relies on the hairlike structures for the majority of it's enviromental awareness.  

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